1
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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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2
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Wu E, Xu G, Xie D, Qiao L. Data-independent acquisition in Metaproteomics. Expert Rev Proteomics 2024. [PMID: 39152734 DOI: 10.1080/14789450.2024.2394190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
INTRODUCTION Metaproteomics offers insights into the function of complex microbial communities while it is also capable of revealing microbe-microbe and host-microbe interactions. Data-independent acquisition (DIA) mass spectrometry is an emerging technology, which holds great potential to achieve deep and accurate metaproteomics with higher reproducibility yet still facing a series of challenges due to the inherent complexity of metaproteomics and DIA data. AREAS COVERED This review offers an overview of the DIA metaproteomics approaches, covering aspects such as database construction, search strategy, and data analysis tools. Several cases of current DIA metaproteomics studies are presented to illustrate the procedures. Important ongoing challenges are also highlighted. Future perspectives of DIA methods for metaproteomics analysis are further discussed. Cited references are searched through and collected from Google Scholar and PubMed. EXPERT OPINION Considering the inherent complexity of DIA metaproteomics data, data analysis strategies specifically designed for interpretation is imperative. From this point of view, we anticipate that deep learning methods and de novo sequencing methods will become more prevalent in the future, potentially improving protein coverage in metaproteomics. Moreover, the advancement of metaproteomics also depends on the development of sample preparation methods, data analysis strategies, etc. These factors are key to unlocking the full potential of metaproteomics.
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Affiliation(s)
- Enhui Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Chemistry, Fudan University, Shanghai, China
| | - Guanyang Xu
- Department of Chemistry, Fudan University, Shanghai, China
| | - Dong Xie
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liang Qiao
- Department of Chemistry, Fudan University, Shanghai, China
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3
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Flender D, Vilenne F, Adams C, Boonen K, Valkenborg D, Baggerman G. Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39152539 DOI: 10.1002/mas.21905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/19/2024]
Abstract
Immunopeptidomics is becoming an increasingly important field of study. The capability to identify immunopeptides with pivotal roles in the human immune system is essential to shift the current curative medicine towards personalized medicine. Throughout the years, the field has matured, giving insight into the current pitfalls. Nowadays, it is commonly accepted that generalizing shotgun proteomics workflows is malpractice because immunopeptidomics faces numerous challenges. While many of these difficulties have been addressed, the road towards the ideal workflow remains complicated. Although the presence of Posttranslational modifications (PTMs) in the immunopeptidome has been demonstrated, their identification remains highly challenging despite their significance for immunotherapies. The large number of unpredictable modifications in the immunopeptidome plays a pivotal role in the functionality and these challenges. This review provides a comprehensive overview of the current advancements in immunopeptidomics. We delve into the challenges associated with identifying PTMs within the immunopeptidome, aiming to address the current state of the field.
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Affiliation(s)
- Daniel Flender
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- Health Unit, VITO, Mol, Belgium
| | - Frédérique Vilenne
- Health Unit, VITO, Mol, Belgium
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- ImmuneSpec, Niel, Belgium
| | - Dirk Valkenborg
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Geert Baggerman
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
- ImmuneSpec, Niel, Belgium
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4
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Langbøl M, Saruhanian A, Saruhanian S, Tiedemann D, Baskaran T, Vohra R, Rives AS, Prokosch V, Liu H, Lackmann JW, Müller S, Nielsen CH, Kolko M, Rovelt J. Proteomic and Cytokine Profiling in Plasma from Patients with Normal-Tension Glaucoma and Ocular Hypertension. Cell Mol Neurobiol 2024; 44:59. [PMID: 39150567 PMCID: PMC11329415 DOI: 10.1007/s10571-024-01492-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024]
Abstract
Primary open-angle glaucoma (POAG) is subdivided depending on eye pressure. Patients with normal-tension glaucoma (NTG) have never had high intraocular pressure (IOP) measured while patients with ocular hypertension (OHT) have high eye pressure but no signs of glaucoma. Although IOP is considered to be a risk factor for all glaucoma patients, it is reasonable to assume that other risk factors such as inflammation play a role. We aimed to characterize the proteome and cytokine profile during hypoxia in plasma from patients with NTG (n = 10), OHT (n = 10), and controls (n = 10). Participants were exposed to hypoxia for two hours, followed by 30 min of normoxia. Samples were taken before ("baseline"), during ("hypoxia"), and after hypoxia ("recovery"). Proteomics based on liquid chromatography coupled with mass spectrometry (LC-MS) was performed. Cytokines were measured by Luminex assays. Bioinformatic analyses indicated the involvement of complement and coagulation cascades in NTG and OHT. Regulation of high-density lipoprotein 3 (HDL3) apolipoproteins suggested that changes in cholesterol metabolism are related to OHT. Hypoxia decreased the level of tumor necrosis factor-α (TNF-α) in OHT patients compared to controls. Circulating levels of interleukin-1β (IL-1β) and C-reactive protein (CRP) were decreased in NTG patients compared to controls during hypoxia. After recovery, plasma interleukin-6 (IL-6) was upregulated in patients with NTG and OHT. Current results indicate an enhanced systemic immune response in patients with NTG and OHT, which correlates with pathogenic events in glaucoma. Apolipoproteins may have anti-inflammatory effects, enabling OHT patients to withstand inflammation and development of glaucoma despite high IOP.
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Affiliation(s)
- Mia Langbøl
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark.
| | - Arevak Saruhanian
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - Sarkis Saruhanian
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Veterinary & Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Daniel Tiedemann
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Thisayini Baskaran
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - Rupali Vohra
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Amalie Santaolalla Rives
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - Verena Prokosch
- Department of Ophthalmology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937, Cologne, Germany
| | - Hanhan Liu
- Department of Ophthalmology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937, Cologne, Germany
| | - Jan-Wilm Lackmann
- CECAD/CMMC Proteomics Facility, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Stefan Müller
- CECAD/CMMC Proteomics Facility, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Claus Henrik Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Miriam Kolko
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Jens Rovelt
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
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5
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Beltrao P, Van Den Bossche T, Gabriels R, Holstein T, Kockmann T, Nameni A, Panse C, Schlapbach R, Lautenbacher L, Mattanovich M, Nesvizhskii A, Van Puyvelde B, Scheid J, Schwämmle V, Strauss M, Susmelj AK, The M, Webel H, Wilhelm M, Winkelhardt D, Wolski WE, Xi M. Proceedings of the EuBIC-MS developers meeting 2023. J Proteomics 2024; 305:105246. [PMID: 38964537 DOI: 10.1016/j.jprot.2024.105246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/19/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024]
Abstract
The 2023 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers Meeting was held from January 15th to January 20th, 2023, in Congressi Stefano Franscin at Monte Verità in Ticino, Switzerland. The participants were scientists and developers working in computational mass spectrometry (MS), metabolomics, and proteomics. The 5-day program was split between introductory keynote lectures and parallel hackathon sessions focusing on "Artificial Intelligence in proteomics" to stimulate future directions in the MS-driven omics areas. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts and actively contribute to highly relevant research projects. We successfully produced several new tools applicable to the proteomics community by improving data analysis and facilitating future research.
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Affiliation(s)
| | - Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, 9052 Zwijnaarde, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, 9052 Zwijnaarde, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Tanja Holstein
- VIB-UGent Center for Medical Biotechnology, 9052 Zwijnaarde, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Tobias Kockmann
- Functional Genomics Center Zürich, ETH Zürich/University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Alireza Nameni
- VIB-UGent Center for Medical Biotechnology, 9052 Zwijnaarde, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Christian Panse
- Functional Genomics Center Zürich, ETH Zürich/University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland.
| | - Ralph Schlapbach
- Functional Genomics Center Zürich, ETH Zürich/University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Ludwig Lautenbacher
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, D - 85354 Freising, Germany
| | - Matthias Mattanovich
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Alexey Nesvizhskii
- Departments of Pathology and Computational Medicine and Bioinfoirmatics, University of Michigan, Ann Arbor, MI 48105, USA
| | - Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, BE-9000 Ghent, Belgium
| | - Jonas Scheid
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University hospital Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany; Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Maximilian Strauss
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Matthew The
- TUM School of Life Sciences Technische Universität München, D - 85354 Freising, Germany
| | - Henry Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, D - 85354 Freising, Germany
| | | | - Witold E Wolski
- Functional Genomics Center Zürich, ETH Zürich/University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Muyao Xi
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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6
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Hutchins PD, Saez Cabezas CA, Enokida JS, Hu Y, Lai Y, Mazure V, Martin M, Setula K, Stutzman JR, Wade JH. Monitoring Epoxidized Soybean Oil Degradation Using Liquid Chromatography-Mass Spectrometry and In Silico Spectral Libraries. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1940-1949. [PMID: 39043119 DOI: 10.1021/jasms.4c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Epoxidized soybean oil (ESO) is routinely used as a bioderived plasticizer and stabilizer in polyvinyl chloride (PVC), as it prolongs material integrity during dehydrochlorination. During this process, the epoxide moieties of ESO are progressively converted to chlorohydrins, which amplify ESO's inherent structural complexity. Past characterization efforts utilized separation-mass spectrometry (MS) analysis of the hydrolyzed acyl chains to simplify the complexity. However, this approach significantly increases the complexity of sample preparation and cannot directly monitor the chlorination of individual ESO species during aging. Here, we present a comprehensive LC-MS/MS data acquisition and in silico spectral library identification workflow optimized for intact ESO byproduct analysis. Detailed MS/MS fragmentation rules derived from synthesized standards were coupled with improved fragment ion intensity modeling capabilities to generate a high-fidelity spectral library for rapid ESO byproduct identification. Identification confidence was further bolstered by using retention time modeling to filter spurious MS/MS matches. Finally, we paired this informatic approach with an optimized extraction procedure and reversed-phase separation to generate a detailed timeline of more than 400 ESO species and byproducts during PVC thermal aging. These developments significantly improve our ability to detect, characterize, and understand ESO degradation in complex PVC formulations with new levels of molecular resolution.
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Affiliation(s)
- Paul D Hutchins
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Camila A Saez Cabezas
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Joshua S Enokida
- Packaging & Specialty Plastics, The Dow Chemical Company, 230 Abner Jackson Pkwy, Lake Jackson, Texas 77566, United States
| | - Yushan Hu
- Packaging & Specialty Plastics, The Dow Chemical Company, 230 Abner Jackson Pkwy, Lake Jackson, Texas 77566, United States
| | - Yuming Lai
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Victoria Mazure
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Marie Martin
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Kelly Setula
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - John R Stutzman
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - James H Wade
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
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7
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Buur LM, Declercq A, Strobl M, Bouwmeester R, Degroeve S, Martens L, Dorfer V, Gabriels R. MS 2Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0. J Proteome Res 2024; 23:3200-3207. [PMID: 38491990 DOI: 10.1021/acs.jproteome.3c00785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Rescoring of peptide-spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need for software maintenance and continuous improvement for such algorithms. We introduce MS2Rescore 3.0, a versatile, modular, and user-friendly platform designed to increase peptide identifications. Researchers can install MS2Rescore across various platforms with minimal effort and benefit from a graphical user interface, a modular Python API, and extensive documentation. To showcase this new version, we connected MS2Rescore 3.0 with MS Amanda 3.0, a new release of the well-established search engine, addressing previous limitations on automatic rescoring. Among new features, MS Amanda now contains additional output columns that can be used for rescoring. The full potential of rescoring is best revealed when applied on challenging data sets. We therefore evaluated the performance of these two tools on publicly available single-cell data sets, where the number of PSMs was substantially increased, thereby demonstrating that MS2Rescore offers a powerful solution to boost peptide identifications. MS2Rescore's modular design and user-friendly interface make data-driven rescoring easily accessible, even for inexperienced users. We therefore expect the MS2Rescore to be a valuable tool for the wider proteomics community. MS2Rescore is available at https://github.com/compomics/ms2rescore.
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Affiliation(s)
- Louise M Buur
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg 4232, Austria
| | - Arthur Declercq
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
| | - Marina Strobl
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg 4232, Austria
| | - Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
| | - Viktoria Dorfer
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg 4232, Austria
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
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8
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Williams G, Couchman L, Taylor DR, Sandhu JK, Slingsby OC, Ng LL, Moniz CF, Jones DJL, Maxwell CB. Use of Nonhuman Sera as a Highly Cost-Effective Internal Standard for Quantitation of Multiple Human Proteins Using Species-Specific Tryptic Peptides: Applicability in Clinical LC-MS Analyses. J Proteome Res 2024; 23:3052-3063. [PMID: 38533909 PMCID: PMC11301776 DOI: 10.1021/acs.jproteome.3c00762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Quantitation of proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS) is complex, with a multiplicity of options ranging from label-free techniques to chemically and metabolically labeling proteins. Increasingly, for clinically relevant analyses, stable isotope-labeled (SIL) internal standards (ISs) represent the "gold standard" for quantitation due to their similar physiochemical properties to the analyte, wide availability, and ability to multiplex to several peptides. However, the purchase of SIL-ISs is a resource-intensive step in terms of cost and time, particularly for screening putative biomarker panels of hundreds of proteins. We demonstrate an alternative strategy utilizing nonhuman sera as the IS for quantitation of multiple human proteins. We demonstrate the effectiveness of this strategy using two high abundance clinically relevant analytes, vitamin D binding protein [Gc globulin] (DBP) and albumin (ALB). We extend this to three putative risk markers for cardiovascular disease: plasma protease C1 inhibitor (SERPING1), annexin A1 (ANXA1), and protein kinase, DNA-activated catalytic subunit (PRKDC). The results show highly specific, reproducible, and linear measurement of the proteins of interest with comparable precision and accuracy to the gold standard SIL-IS technique. This approach may not be applicable to every protein, but for many proteins it can offer a cost-effective solution to LC-MS/MS protein quantitation.
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Affiliation(s)
- Geraldine Williams
- Leicester
van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United
Kingdom
- Department
of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical
Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Lewis Couchman
- Leicester
Cancer Research Centre, RKCSB, University
of Leicester, Leicester LE2 7LX, United Kingdom
- Viapath
Analytics, King’s College Hospital, Denmark Hill, London SE5 9RS, United Kingdom
- Department
of Clinical Biochemistry, King’s
College Hospital, Denmark
Hill, London SE5 9RS, United Kingdom
| | - David R. Taylor
- Viapath
Analytics, King’s College Hospital, Denmark Hill, London SE5 9RS, United Kingdom
| | - Jatinderpal K. Sandhu
- Leicester
van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United
Kingdom
- Department
of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical
Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Oliver C. Slingsby
- Leicester
van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United
Kingdom
- Department
of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical
Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Leong L. Ng
- Leicester
van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United
Kingdom
- Department
of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical
Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Cajetan F. Moniz
- Department
of Clinical Biochemistry, King’s
College Hospital, Denmark
Hill, London SE5 9RS, United Kingdom
| | - Donald J. L. Jones
- Leicester
van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United
Kingdom
- Leicester
Cancer Research Centre, RKCSB, University
of Leicester, Leicester LE2 7LX, United Kingdom
- Department
of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical
Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Colleen B. Maxwell
- Leicester
van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United
Kingdom
- Department
of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical
Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
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9
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Yilmaz M, Fondrie WE, Bittremieux W, Melendez CF, Nelson R, Ananth V, Oh S, Noble WS. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. Nat Commun 2024; 15:6427. [PMID: 39080256 PMCID: PMC11289372 DOI: 10.1038/s41467-024-49731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/18/2024] [Indexed: 08/02/2024] Open
Abstract
A fundamental challenge in mass spectrometry-based proteomics is the identification of the peptide that generated each acquired tandem mass spectrum. Approaches that leverage known peptide sequence databases cannot detect unexpected peptides and can be impractical or impossible to apply in some settings. Thus, the ability to assign peptide sequences to tandem mass spectra without prior information-de novo peptide sequencing-is valuable for tasks including antibody sequencing, immunopeptidomics, and metaproteomics. Although many methods have been developed to address this problem, it remains an outstanding challenge in part due to the difficulty of modeling the irregular data structure of tandem mass spectra. Here, we describe Casanovo, a machine learning model that uses a transformer neural network architecture to translate the sequence of peaks in a tandem mass spectrum into the sequence of amino acids that comprise the generating peptide. We train a Casanovo model from 30 million labeled spectra and demonstrate that the model outperforms several state-of-the-art methods on a cross-species benchmark dataset. We also develop a version of Casanovo that is fine-tuned for non-enzymatic peptides. Finally, we demonstrate that Casanovo's superior performance improves the analysis of immunopeptidomics and metaproteomics experiments and allows us to delve deeper into the dark proteome.
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Affiliation(s)
- Melih Yilmaz
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
| | | | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Carlo F Melendez
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Rowan Nelson
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Varun Ananth
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
| | - Sewoong Oh
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
| | - William Stafford Noble
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA.
- Department of Genome Sciences, University of Washington, Seattle, USA.
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10
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Dens C, Adams C, Laukens K, Bittremieux W. Machine Learning Strategies to Tackle Data Challenges in Mass Spectrometry-Based Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39074335 DOI: 10.1021/jasms.4c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
In computational proteomics, machine learning (ML) has emerged as a vital tool for enhancing data analysis. Despite significant advancements, the diversity of ML model architectures and the complexity of proteomics data present substantial challenges in the effective development and evaluation of these tools. Here, we highlight the necessity for high-quality, comprehensive data sets to train ML models and advocate for the standardization of data to support robust model development. We emphasize the instrumental role of key data sets like ProteomeTools and MassIVE-KB in advancing ML applications in proteomics and discuss the implications of data set size on model performance, highlighting that larger data sets typically yield more accurate models. To address data scarcity, we explore algorithmic strategies such as self-supervised pretraining and multitask learning. Ultimately, we hope that this discussion can serve as a call to action for the proteomics community to collaborate on data standardization and collection efforts, which are crucial for the sustainable advancement and refinement of ML methodologies in the field.
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Affiliation(s)
- Ceder Dens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerpen, Belgium
| | - Charlotte Adams
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerpen, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerpen, Belgium
| | - Wout Bittremieux
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerpen, Belgium
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11
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Kruk ME, Mehta S, Murray K, Higgins L, Do K, Johnson JE, Wagner R, Wendt CH, O’Connor JB, Harris JK, Laguna TA, Jagtap PD, Griffin TJ. An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease. mSystems 2024; 9:e0092923. [PMID: 38934598 PMCID: PMC11264604 DOI: 10.1128/msystems.00929-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Airway microbiota are known to contribute to lung diseases, such as cystic fibrosis (CF), but their contributions to pathogenesis are still unclear. To improve our understanding of host-microbe interactions, we have developed an integrated analytical and bioinformatic mass spectrometry (MS)-based metaproteomics workflow to analyze clinical bronchoalveolar lavage (BAL) samples from people with airway disease. Proteins from BAL cellular pellets were processed and pooled together in groups categorized by disease status (CF vs. non-CF) and bacterial diversity, based on previously performed small subunit rRNA sequencing data. Proteins from each pooled sample group were digested and subjected to liquid chromatography tandem mass spectrometry (MS/MS). MS/MS spectra were matched to human and bacterial peptide sequences leveraging a bioinformatic workflow using a metagenomics-guided protein sequence database and rigorous evaluation. Label-free quantification revealed differentially abundant human peptides from proteins with known roles in CF, like neutrophil elastase and collagenase, and proteins with lesser-known roles in CF, including apolipoproteins. Differentially abundant bacterial peptides were identified from known CF pathogens (e.g., Pseudomonas), as well as other taxa with potentially novel roles in CF. We used this host-microbe peptide panel for targeted parallel-reaction monitoring validation, demonstrating for the first time an MS-based assay effective for quantifying host-microbe protein dynamics within BAL cells from individual CF patients. Our integrated bioinformatic and analytical workflow combining discovery, verification, and validation should prove useful for diverse studies to characterize microbial contributors in airway diseases. Furthermore, we describe a promising preliminary panel of differentially abundant microbe and host peptide sequences for further study as potential markers of host-microbe relationships in CF disease pathogenesis.IMPORTANCEIdentifying microbial pathogenic contributors and dysregulated human responses in airway disease, such as CF, is critical to understanding disease progression and developing more effective treatments. To this end, characterizing the proteins expressed from bacterial microbes and human host cells during disease progression can provide valuable new insights. We describe here a new method to confidently detect and monitor abundance changes of both microbe and host proteins from challenging BAL samples commonly collected from CF patients. Our method uses both state-of-the art mass spectrometry-based instrumentation to detect proteins present in these samples and customized bioinformatic software tools to analyze the data and characterize detected proteins and their association with CF. We demonstrate the use of this method to characterize microbe and host proteins from individual BAL samples, paving the way for a new approach to understand molecular contributors to CF and other diseases of the airway.
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Affiliation(s)
- Monica E. Kruk
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - Kevin Murray
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
- Center for Metabolomics and Proteomics, University of Minnesota, Minneapolis, Minnesota, USA
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
- Center for Metabolomics and Proteomics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Katherine Do
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reid Wagner
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Chris H. Wendt
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
- Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - John B. O’Connor
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children’s Hospital, Seattle, Washington, USA
| | - J. Kirk Harris
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Theresa A. Laguna
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children’s Hospital, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
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12
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Klein J, Carvalho L, Zaia J. Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity. Nat Commun 2024; 15:6168. [PMID: 39039063 PMCID: PMC11263600 DOI: 10.1038/s41467-024-50338-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
Accurate glycopeptide identification in mass spectrometry-based glycoproteomics is a challenging problem at scale. Recent innovation has been made in increasing the scope and accuracy of glycopeptide identifications, with more precise uncertainty estimates for each part of the structure. We present a dynamically adapting relative retention time model for detecting and correcting ambiguous glycan assignments that are difficult to detect from fragmentation alone, a layered approach to glycopeptide fragmentation modeling that improves N-glycopeptide identification in samples without compromising identification quality, and a site-specific method to increase the depth of the glycoproteome confidently identifiable even further. We demonstrate our techniques on a set of previously published datasets, showing the performance gains at each stage of optimization. These techniques are provided in the open-source glycomics and glycoproteomics platform GlycReSoft available at https://github.com/mobiusklein/glycresoft .
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Affiliation(s)
- Joshua Klein
- Program for Bioinformatics, Boston University, Boston, MA, US.
| | - Luis Carvalho
- Program for Bioinformatics, Boston University, Boston, MA, US
- Department of Math and Statistics, Boston University, Boston, MA, US
| | - Joseph Zaia
- Program for Bioinformatics, Boston University, Boston, MA, US.
- Department of Biochemistry and Cell Biology, Boston University, Boston, MA, US.
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13
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Villa C, Secchi V, Macchi M, Tripodi L, Trombetta E, Zambroni D, Padelli F, Mauri M, Molinaro M, Oddone R, Farini A, De Palma A, Varela Pinzon L, Santarelli F, Simonutti R, Mauri P, Porretti L, Campione M, Aquino D, Monguzzi A, Torrente Y. Magnetic-field-driven targeting of exosomes modulates immune and metabolic changes in dystrophic muscle. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01725-y. [PMID: 39039121 DOI: 10.1038/s41565-024-01725-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 06/18/2024] [Indexed: 07/24/2024]
Abstract
Exosomes are promising therapeutics for tissue repair and regeneration to induce and guide appropriate immune responses in dystrophic pathologies. However, manipulating exosomes to control their biodistribution and targeting them in vivo to achieve adequate therapeutic benefits still poses a major challenge. Here we overcome this limitation by developing an externally controlled delivery system for primed annexin A1 myo-exosomes (Exomyo). Effective nanocarriers are realized by immobilizing the Exomyo onto ferromagnetic nanotubes to achieve controlled delivery and localization of Exomyo to skeletal muscles by systemic injection using an external magnetic field. Quantitative muscle-level analyses revealed that macrophages dominate the uptake of Exomyo from these ferromagnetic nanotubes in vivo to synergistically promote beneficial muscle responses in a murine animal model of Duchenne muscular dystrophy. Our findings provide insights into the development of exosome-based therapies for muscle diseases and, in general, highlight the formulation of effective functional nanocarriers aimed at optimizing exosome biodistribution.
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Affiliation(s)
- Chiara Villa
- Stem Cell Laboratory, Dino Ferrari Center, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Valeria Secchi
- Department of Materials Science, University of Milano Bicocca, Milan, Italy
- NANOMIB, Nanomedicine Center, University of Milano Bicocca, Milan, Italy
| | - Mirco Macchi
- Stem Cell Laboratory, Dino Ferrari Center, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Luxembourg Centre for Systems Biomedicine, Department of Biomedical Data Science, Luxembourg City, Luxembourg
| | - Luana Tripodi
- Stem Cell Laboratory, Dino Ferrari Center, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Elena Trombetta
- Flow Cytometry Service, Clinical Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Desiree Zambroni
- Advanced Light and Electron Microscopy Bioimaging Center ALEMBIC, San Raffaele Scientific Institute - OSR, Milan, Italy
| | - Francesco Padelli
- Department of Neuroradiology, IRCCS Foundation Neurological Institute 'Carlo Besta', Milan, Italy
| | - Michele Mauri
- Department of Materials Science, University of Milano Bicocca, Milan, Italy
- NANOMIB, Nanomedicine Center, University of Milano Bicocca, Milan, Italy
| | - Monica Molinaro
- Stem Cell Laboratory, Dino Ferrari Center, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Rebecca Oddone
- Stem Cell Laboratory, Dino Ferrari Center, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Andrea Farini
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonella De Palma
- National Research Council of Italy, Proteomics and Metabolomics Unit, Institute for Biomedical Technologies, ITB-CNR, Segrate, Milan, Italy
- Clinical Proteomics Laboratory, ITB-CNR, CNR.Biomics Infrastructure, Elixir, Milan, Italy
| | - Laura Varela Pinzon
- Veterinary Medicine, Department Clinical Sciences, Equine Sciences, Equine Musculoskeletal Biology. Utrecht University, Utrecht, Netherlands
| | - Federica Santarelli
- Stem Cell Laboratory, Dino Ferrari Center, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Roberto Simonutti
- Department of Materials Science, University of Milano Bicocca, Milan, Italy
- NANOMIB, Nanomedicine Center, University of Milano Bicocca, Milan, Italy
| | - PierLuigi Mauri
- National Research Council of Italy, Proteomics and Metabolomics Unit, Institute for Biomedical Technologies, ITB-CNR, Segrate, Milan, Italy
- Clinical Proteomics Laboratory, ITB-CNR, CNR.Biomics Infrastructure, Elixir, Milan, Italy
| | - Laura Porretti
- Flow Cytometry Service, Clinical Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marcello Campione
- NANOMIB, Nanomedicine Center, University of Milano Bicocca, Milan, Italy
- Department of Earth and Environmental Sciences, University of Milano Bicocca, Milano, Italy
| | - Domenico Aquino
- Department of Neuroradiology, IRCCS Foundation Neurological Institute 'Carlo Besta', Milan, Italy
| | - Angelo Monguzzi
- Department of Materials Science, University of Milano Bicocca, Milan, Italy
- NANOMIB, Nanomedicine Center, University of Milano Bicocca, Milan, Italy
| | - Yvan Torrente
- Stem Cell Laboratory, Dino Ferrari Center, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
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14
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Searle B, Shannon A, Teodorescu R, Song NJ, Heil L, Jacob C, Remes P, Li Z, Rubinstein M. Rapid assay development for low input targeted proteomics using a versatile linear ion trap. RESEARCH SQUARE 2024:rs.3.rs-4702746. [PMID: 39070662 PMCID: PMC11275998 DOI: 10.21203/rs.3.rs-4702746/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Advances in proteomics and mass spectrometry enable the study of limited cell populations, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive low-mass accuracy measurements, these instruments are effectively restricted to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. Here, we describe a workflow using a new hybrid quadrupole-LIT instrument that rapidly develops targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Using an automated software approach for scheduling parallel reaction monitoring assays (PRM), we show consistent quantification across three orders of magnitude in a matched-matrix background. We demonstrate measuring low-level proteins such as transcription factors and cytokines with quantitative linearity below two orders of magnitude in a 1 ng background proteome without requiring stable isotope-labeled standards. From a 1 ng sample, we found clear consistency between proteins in subsets of CD4+ and CD8+ T cells measured using high dimensional flow cytometry and LIT-based proteomics. Based on these results, we believe hybrid quadrupole-LIT instruments represent an economical solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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Affiliation(s)
| | | | | | | | | | | | | | - Zihai Li
- The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute
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15
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Korchak JA, Jeffery ED, Bandyopadhyay S, Jordan BT, Lehe MD, Watts EF, Fenix A, Wilhelm M, Sheynkman GM. IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39012054 DOI: 10.1021/jasms.4c00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Alternative splicing is a major contributor of transcriptomic complexity, but the extent to which transcript isoforms are translated into stable, functional protein isoforms is unclear. Furthermore, detection of relatively scarce isoform-specific peptides is challenging, with many protein isoforms remaining uncharted due to technical limitations. Recently, a family of advanced targeted MS strategies, termed internal standard parallel reaction monitoring (IS-PRM), have demonstrated multiplexed, sensitive detection of predefined peptides of interest. Such approaches have not yet been used to confirm existence of novel peptides. Here, we present a targeted proteogenomic approach that leverages sample-matched long-read RNA sequencing (lrRNA-seq) data to predict potential protein isoforms with prior transcript evidence. Predicted tryptic isoform-specific peptides, which are specific to individual gene product isoforms, serve as "triggers" and "targets" in the IS-PRM method, Tomahto. Using the model human stem cell line WTC11, LR RNaseq data were generated and used to inform the generation of synthetic standards for 192 isoform-specific peptides (114 isoforms from 55 genes). These synthetic "trigger" peptides were labeled with super heavy tandem mass tags (TMT) and spiked into TMT-labeled WTC11 tryptic digest, predicted to contain corresponding endogenous "target" peptides. Compared to DDA mode, Tomahto increased detectability of isoforms by 3.6-fold, resulting in the identification of five previously unannotated isoforms. Our method detected protein isoform expression for 43 out of 55 genes corresponding to 54 resolved isoforms. This lrRNA-seq-informed Tomahto targeted approach is a new modality for generating protein-level evidence of alternative isoforms─a critical first step in designing functional studies and eventually clinical assays.
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Affiliation(s)
- Jennifer A Korchak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Saikat Bandyopadhyay
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, United States
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Ben T Jordan
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Micah D Lehe
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Emily F Watts
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Aidan Fenix
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, United States
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22903, United States
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia 22903, United States
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16
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Sairenji TJ, Masuda S, Higuchi Y, Miyazaki M, Yajima H, Kwan Ee O, Fujiwara Y, Araki T, Shimokawa N, Koibuchi N. Plasma prolactin axis shift from placental to pituitary origin in late prepartum mice. Endocr J 2024; 71:661-674. [PMID: 38749736 DOI: 10.1507/endocrj.ej23-0724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/17/2024] Open
Abstract
The placenta secretes a prolactin (PRL)-like hormone PRL3B1 (placental lactogen II), a luteotropic hormone essential for maintaining pregnancy until labor in mice. A report from 1984 examined the secretion pattern of PRL3B1 in prepartum mice. In the current study, we found contradictory findings in the secretion pattern that invalidate the previous report. By measuring maternal plasma PRL3B1 and PRL every 4 hrs from gestational day 17 (G17), we newly discovered that maternal plasma PRL3B1 levels decrease rapidly in prepartum C57BL/6 mice. Interestingly, the onset of this decline coincided with the PRL surge at G18, demonstrating a plasma prolactin axis shift from placental to pituitary origin. We also found that maternal plasma progesterone regression precedes the onset of the PRL shift. The level of Prl3b1 mRNA was determined by RT-qPCR in the placenta and remained stable until parturition, implying that PRL3B1 peptide production or secretion was suppressed. We hypothesized that production of the PRL family, the 25 paralogous PRL proteins exclusively expressed in mice placenta, would decrease alongside PRL3B1 during this period. To investigate this hypothesis and to seek proteomic changes, we performed a shotgun proteome analysis of the placental tissue using data-independent acquisition mass spectrometry (DIA-MS). Up to 5,891 proteins were identified, including 17 PRL family members. Relative quantitative analysis between embryonic day 17 (E17) and E18 placentas showed no significant difference in the expression of PRL3B1 and most PRL family members except PRL7C1. These results suggest that PRL3B1 secretion from the placenta is suppressed at G18 (E18).
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Affiliation(s)
- Taku James Sairenji
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Shinnosuke Masuda
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
- Laboratory of Epigenetics and Metabolism, Institute of Molecular and Cellular Regulations, Gunma 371-8512, Japan
| | - Yuya Higuchi
- Department of Clinical Pharmacology and Therapeutics, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Mitsue Miyazaki
- Department of Clinical Pharmacology and Therapeutics, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
- Department of Bioscience and Laboratory Medicine, Hirosaki University Graduate School of Health Sciences, Aomori 036-8564, Japan
- Department of Nutrition, Takasaki University of Health and Welfare, Gunma 370-0033, Japan
| | - Hiroyuki Yajima
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Oh Kwan Ee
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Yuki Fujiwara
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Takuya Araki
- Department of Clinical Pharmacology and Therapeutics, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Noriaki Shimokawa
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
- Department of Nutrition, Takasaki University of Health and Welfare, Gunma 370-0033, Japan
| | - Noriyuki Koibuchi
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
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17
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Garcia-Vilanova A, Allué-Guardia A, Chacon NM, Akhter A, Singh DK, Kaushal D, Restrepo BI, Schlesinger LS, Turner J, Weintraub ST, Torrelles JB. Proteomic analysis of lung responses to SARS-CoV-2 infection in aged non-human primates: clinical and research relevance. GeroScience 2024:10.1007/s11357-024-01264-3. [PMID: 38969861 DOI: 10.1007/s11357-024-01264-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
With devastating health and socioeconomic impact worldwide, much work is left to understand the Coronavirus Disease 2019 (COVID-19), with emphasis in the severely affected elderly population. Here, we present a proteomics study of lung tissue obtained from aged vs. young rhesus macaques (Macaca mulatta) and olive baboons (Papio Anubis) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using age as a variable, we identified common proteomic profiles in the lungs of aged infected non-human primates (NHPs), including key regulators of immune function, as well as cell and tissue remodeling, and discuss the potential clinical relevance of such parameters. Further, we identified key differences in proteomic profiles between both NHP species, and compared those to what is known about SARS-CoV-2 in humans. Finally, we explored the translatability of these animal models in the context of aging and the human presentation of the COVID-19.
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Affiliation(s)
- Andreu Garcia-Vilanova
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Anna Allué-Guardia
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA.
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Nadine M Chacon
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
- Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Anwari Akhter
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Dhiraj Kumar Singh
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Deepak Kaushal
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Blanca I Restrepo
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA
- University of Texas Health Science Center at Houston, School of Public Health, Brownsville Campus, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Larry S Schlesinger
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Joanne Turner
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA
- Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jordi B Torrelles
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA.
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA.
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18
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Taurozzi AJ, Rüther PL, Patramanis I, Koenig C, Sinclair Paterson R, Madupe PP, Harking FS, Welker F, Mackie M, Ramos-Madrigal J, Olsen JV, Cappellini E. Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel. Nat Protoc 2024; 19:2085-2116. [PMID: 38671208 DOI: 10.1038/s41596-024-00975-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/12/2024] [Indexed: 04/28/2024]
Abstract
In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient DNA preservation in the same areas. Accordingly, their amino acid sequences currently represent the only source of genetic information available to pursue phylogenetic inference involving species that went extinct too long ago to be amenable for ancient DNA analysis. Here we present a complete workflow, including sample preparation, mass spectrometric data acquisition and computational analysis, to recover and interpret million-year-old dental enamel protein sequences. During sample preparation, the proteolytic digestion step, usually an integral part of conventional bottom-up proteomics, is omitted to increase the recovery of the randomly degraded peptides spontaneously generated by extensive diagenetic hydrolysis of ancient proteins over geological time. Similarly, we describe other solutions we have adopted to (1) authenticate the endogenous origin of the protein traces we identify, (2) detect and validate amino acid variation in the ancient protein sequences and (3) attempt phylogenetic inference. Sample preparation and data acquisition can be completed in 3-4 working days, while subsequent data analysis usually takes 2-5 days. The workflow described requires basic expertise in ancient biomolecules analysis, mass spectrometry-based proteomics and molecular phylogeny. Finally, we describe the limits of this approach and its potential for the reconstruction of evolutionary relationships in paleontology and paleoanthropology.
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Affiliation(s)
| | - Patrick L Rüther
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Palesa P Madupe
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Florian Simon Harking
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Meaghan Mackie
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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19
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Smith BJ, Guest PC, Martins-de-Souza D. Maximizing Analytical Performance in Biomolecular Discovery with LC-MS: Focus on Psychiatric Disorders. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:25-46. [PMID: 38424029 DOI: 10.1146/annurev-anchem-061522-041154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
In this review, we discuss the cutting-edge developments in mass spectrometry proteomics and metabolomics that have brought improvements for the identification of new disease-based biomarkers. A special focus is placed on psychiatric disorders, for example, schizophrenia, because they are considered to be not a single disease entity but rather a spectrum of disorders with many overlapping symptoms. This review includes descriptions of various types of commonly used mass spectrometry platforms for biomarker research, as well as complementary techniques to maximize data coverage, reduce sample heterogeneity, and work around potentially confounding factors. Finally, we summarize the different statistical methods that can be used for improving data quality to aid in reliability and interpretation of proteomics findings, as well as to enhance their translatability into clinical use and generalizability to new data sets.
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Affiliation(s)
- Bradley J Smith
- 1Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, São Paulo, Brazil;
| | - Paul C Guest
- 1Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, São Paulo, Brazil;
- 2Department of Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- 3Laboratory of Translational Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Daniel Martins-de-Souza
- 1Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, São Paulo, Brazil;
- 4Experimental Medicine Research Cluster, University of Campinas, São Paulo, Brazil
- 5National Institute of Biomarkers in Neuropsychiatry, National Council for Scientific and Technological Development, São Paulo, Brazil
- 6D'Or Institute for Research and Education, São Paulo, Brazil
- 7INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil
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20
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Zhang Y, Hu C, Wu X, Song J. Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data. Bioinformatics 2024; 40:btae417. [PMID: 38960865 PMCID: PMC11223842 DOI: 10.1093/bioinformatics/btae417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/27/2024] [Accepted: 07/02/2024] [Indexed: 07/05/2024] Open
Abstract
MOTIVATION The data independent acquisition (DIA) mass spectrometry (MS) method is increasingly popular in the field of proteomics. But the loss of the correspondence between peptide ions and their spectra in DIA makes the identification challenging. One effective approach to reduce false positive identification is to calculate the deviation between the peptide's estimated retention time (RT) and measured RT. During this process, scaling the spectral library RT into the estimated RT, known as the RT calibration, is a prerequisite for calculating the deviation. Currently, within the DIA algorithm ecosystem, there is a lack of engine-independent and readily usable RT calibration toolkits. RESULTS In this work, we introduce Calib-RT, a RT calibration method tailored to the characteristics of RT data. This method can achieve the nonlinear calibration across various data scales and tolerate a certain level of noise interference. Calib-RT is expected to enrich the open source DIA algorithm toolchain and assist in the development of DIA identification algorithms. AVAILABILITY AND IMPLEMENTATION Calib-RT is released as an open source software under the MIT license and can be installed from PyPi as a python module. The source code is available on GitHub at https://github.com/chenghui03/Calib_RT.
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Affiliation(s)
- Yichi Zhang
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Chenghui Hu
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Xiaohui Wu
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Jian Song
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
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21
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Kalhor M, Lapin J, Picciani M, Wilhelm M. Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification. Mol Cell Proteomics 2024; 23:100798. [PMID: 38871251 PMCID: PMC11269915 DOI: 10.1016/j.mcpro.2024.100798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/26/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024] Open
Abstract
Rescoring of peptide spectrum matches originating from database search engines enabled by peptide property predictors is exceeding the performance of peptide identification from traditional database search engines. In contrast to the peptide spectrum match scores calculated by traditional database search engines, rescoring peptide spectrum matches generates scores based on comparing observed and predicted peptide properties, such as fragment ion intensities and retention times. These newly generated scores enable a more efficient discrimination between correct and incorrect peptide spectrum matches. This approach was shown to lead to substantial improvements in the number of confidently identified peptides, facilitating the analysis of challenging datasets in various fields such as immunopeptidomics, metaproteomics, proteogenomics, and single-cell proteomics. In this review, we summarize the key elements leading up to the recent introduction of multiple data-driven rescoring pipelines. We provide an overview of relevant post-processing rescoring tools, introduce prominent data-driven rescoring pipelines for various applications, and highlight limitations, opportunities, and future perspectives of this approach and its impact on mass spectrometry-based proteomics.
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Affiliation(s)
- Mostafa Kalhor
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Joel Lapin
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mario Picciani
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Munich Data Science Institute, Technical University of Munich, Garching, Germany.
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22
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He G, He Q, Cheng J, Yu R, Shuai J, Cao Y. ProPept-MT: A Multi-Task Learning Model for Peptide Feature Prediction. Int J Mol Sci 2024; 25:7237. [PMID: 39000344 PMCID: PMC11241495 DOI: 10.3390/ijms25137237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
In the realm of quantitative proteomics, data-independent acquisition (DIA) has emerged as a promising approach, offering enhanced reproducibility and quantitative accuracy compared to traditional data-dependent acquisition (DDA) methods. However, the analysis of DIA data is currently hindered by its reliance on project-specific spectral libraries derived from DDA analyses, which not only limits proteome coverage but also proves to be a time-intensive process. To overcome these challenges, we propose ProPept-MT, a novel deep learning-based multi-task prediction model designed to accurately forecast key features such as retention time (RT), ion intensity, and ion mobility (IM). Leveraging advanced techniques such as multi-head attention and BiLSTM for feature extraction, coupled with Nash-MTL for gradient coordination, ProPept-MT demonstrates superior prediction performance. Integrating ion mobility alongside RT, mass-to-charge ratio (m/z), and ion intensity forms 4D proteomics. Then, we outline a comprehensive workflow tailored for 4D DIA proteomics research, integrating the use of 4D in silico libraries predicted by ProPept-MT. Evaluation on a benchmark dataset showcases ProPept-MT's exceptional predictive capabilities, with impressive results including a 99.9% Pearson correlation coefficient (PCC) for RT prediction, a median dot product (DP) of 96.0% for fragment ion intensity prediction, and a 99.3% PCC for IM prediction on the test set. Notably, ProPept-MT manifests efficacy in predicting both unmodified and phosphorylated peptides, underscoring its potential as a valuable tool for constructing high-quality 4D DIA in silico libraries.
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Affiliation(s)
- Guoqiang He
- Postgraduate Training Base Alliance, Wenzhou Medical University, Wenzhou 325000, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Qingzu He
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Jinyan Cheng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Rongwen Yu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Jianwei Shuai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Yi Cao
- Postgraduate Training Base Alliance, Wenzhou Medical University, Wenzhou 325000, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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23
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Fröhlich K, Fahrner M, Brombacher E, Seredynska A, Maldacker M, Kreutz C, Schmidt A, Schilling O. Data-independent acquisition: A milestone and prospect in clinical mass spectrometry-based proteomics. Mol Cell Proteomics 2024:100800. [PMID: 38880244 DOI: 10.1016/j.mcpro.2024.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
Data-independent acquisition (DIA) has revolutionized the field of mass spectrometry (MS)-based proteomics over the past few years. DIA stands out for its ability to systematically sample all peptides in a given mass-to-charge range, allowing an unbiased acquisition of proteomics data. This greatly mitigates the issue of missing values and significantly enhances quantitative accuracy, precision, and reproducibility compared to many traditional methods. This review focuses on the critical role of DIA analysis software tools, primarily focusing on their capabilities and the challenges they address in proteomic research. Advances in MS technology, such as trapped ion mobility spectrometry, or high field asymmetric waveform ion mobility spectrometry require sophisticated analysis software capable of handling the increased data complexity and exploiting the full potential of DIA. We identify and critically evaluate leading software tools in the DIA landscape, discussing their unique features, and the reliability of their quantitative and qualitative outputs. We present the biological and clinical relevance of DIA-MS and discuss crucial publications that paved the way for in-depth proteomic characterization in patient-derived specimens. Furthermore, we provide a perspective on emerging trends in clinical applications and present upcoming challenges including standardization and certification of MS-based acquisition strategies in molecular diagnostics. While we emphasize the need for continuous development of software tools to keep pace with evolving technologies, we advise researchers against uncritically accepting the results from DIA software tools. Each tool may have its own biases, and some may not be as sensitive or reliable as others. Our overarching recommendation for both researchers and clinicians is to employ multiple DIA analysis tools, utilizing orthogonal analysis approaches to enhance the robustness and reliability of their findings.
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Affiliation(s)
- Klemens Fröhlich
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
| | - Eva Brombacher
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Adrianna Seredynska
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Maximilian Maldacker
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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24
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Hamaneh M, Ogurtsov AY, Obolensky OI, Yu YK. Systematic Assessment of Deep Learning-Based Predictors of Fragmentation Intensity Profiles. J Proteome Res 2024; 23:1983-1999. [PMID: 38728051 PMCID: PMC11165591 DOI: 10.1021/acs.jproteome.3c00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/05/2024] [Accepted: 04/16/2024] [Indexed: 06/13/2024]
Abstract
In recent years, several deep learning-based methods have been proposed for predicting peptide fragment intensities. This study aims to provide a comprehensive assessment of six such methods, namely Prosit, DeepMass:Prism, pDeep3, AlphaPeptDeep, Prosit Transformer, and the method proposed by Guan et al. To this end, we evaluated the accuracy of the predicted intensity profiles for close to 1.7 million precursors (including both tryptic and HLA peptides) corresponding to more than 18 million experimental spectra procured from 40 independent submissions to the PRIDE repository that were acquired for different species using a variety of instruments and different dissociation types/energies. Specifically, for each method, distributions of similarity (measured by Pearson's correlation and normalized angle) between the predicted and the corresponding experimental b and y fragment intensities were generated. These distributions were used to ascertain the prediction accuracy and rank the prediction methods for particular types of experimental conditions. The effect of variables like precursor charge, length, and collision energy on the prediction accuracy was also investigated. In addition to prediction accuracy, the methods were evaluated in terms of prediction speed. The systematic assessment of these six methods may help in choosing the right method for MS/MS spectra prediction for particular needs.
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Affiliation(s)
- Mehdi
B. Hamaneh
- National Center for Biotechnology
Information, National Library of Medicine,
National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Aleksey Y. Ogurtsov
- National Center for Biotechnology
Information, National Library of Medicine,
National Institutes of Health, Bethesda, Maryland 20894, United States
| | | | - Yi-Kuo Yu
- National Center for Biotechnology
Information, National Library of Medicine,
National Institutes of Health, Bethesda, Maryland 20894, United States
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25
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Wen B, Freestone J, Riffle M, MacCoss MJ, Noble WS, Keich U. Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596967. [PMID: 38895431 PMCID: PMC11185562 DOI: 10.1101/2024.06.01.596967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
A pressing statistical challenge in the field of mass spectrometry proteomics is how to assess whether a given software tool provides accurate error control. Each software tool for searching such data uses its own internally implemented methodology for reporting and controlling the error. Many of these software tools are closed source, with incompletely documented methodology, and the strategies for validating the error are inconsistent across tools. In this work, we identify three different methods for validating false discovery rate (FDR) control in use in the field, one of which is invalid, one of which can only provide a lower bound rather than an upper bound, and one of which is valid but under-powered. The result is that the field has a very poor understanding of how well we are doing with respect to FDR control, particularly for the analysis of data-independent acquisition (DIA) data. We therefore propose a new, more powerful method for evaluating FDR control in this setting, and we then employ that method, along with an existing lower bounding technique, to characterize a variety of popular search tools. We find that the search tools for analysis of data-dependent acquisition (DDA) data generally seem to control the FDR at the peptide level, whereas none of the DIA search tools consistently controls the FDR at the peptide level across all the datasets we investigated. Furthermore, this problem becomes much worse when the latter tools are evaluated at the protein level. These results may have significant implications for various downstream analyses, since proper FDR control has the potential to reduce noise in discovery lists and thereby boost statistical power.
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Affiliation(s)
- Bo Wen
- Department of Genome Sciences, University of Washington
| | - Jack Freestone
- School of Mathematics and Statistics, University of Sydney
| | | | | | - William S Noble
- Department of Genome Sciences, University of Washington
- Paul G. Allen School of Computer Science and Engineering, University of Washington
| | - Uri Keich
- School of Mathematics and Statistics, University of Sydney
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26
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Lautenbacher L, Yang KL, Kockmann T, Panse C, Chambers M, Kahl E, Yu F, Gabriel W, Bold D, Schmidt T, Li K, MacLean B, Nesvizhskii AI, Wilhelm M. Koina: Democratizing machine learning for proteomics research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596953. [PMID: 38895358 PMCID: PMC11185529 DOI: 10.1101/2024.06.01.596953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Recent developments in machine-learning (ML) and deep-learning (DL) have immense potential for applications in proteomics, such as generating spectral libraries, improving peptide identification, and optimizing targeted acquisition modes. Although new ML/DL models for various applications and peptide properties are frequently published, the rate at which these models are adopted by the community is slow, which is mostly due to technical challenges. We believe that, for the community to make better use of state-of-the-art models, more attention should be spent on making models easy to use and accessible by the community. To facilitate this, we developed Koina, an open-source containerized, decentralized and online-accessible high-performance prediction service that enables ML/DL model usage in any pipeline. Using the widely used FragPipe computational platform as example, we show how Koina can be easily integrated with existing proteomics software tools and how these integrations improve data analysis.
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Affiliation(s)
- Ludwig Lautenbacher
- Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany
| | - Kevin L. Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Tobias Kockmann
- Functional Genomics Center Zurich (FGCZ) - University of Zurich | ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Christian Panse
- Functional Genomics Center Zurich (FGCZ) - University of Zurich | ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, CH-1015 Lausanne, Switzerland
| | - Matthew Chambers
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Elias Kahl
- Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany
| | - Fengchao Yu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Wassim Gabriel
- Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany
| | - Dulguun Bold
- Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany
| | | | - Kai Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany
- Munich Data Science Institute, Technical University of Munich, 85748, Garching, Germany
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27
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Yannone SM, Tuteja V, Goleva O, Leung DYM, Stotland A, Keoseyan AJ, Hendricks NG, Van Eyk JE, Kreimer S. Blood to Biomarker Quantitation in Under One Hour with Rapid Proteomics using a Hyperthermoacidic Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596979. [PMID: 38853916 PMCID: PMC11160709 DOI: 10.1101/2024.06.01.596979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Multi-step multi-hour tryptic proteolysis has limited the utility of bottom-up proteomics for cases that require immediate quantitative information. The recently available hyperthermoacidic (HTA) protease "Krakatoa" digests samples in a single 5 to 30-minute step at pH 3 and >80 °C; conditions that disrupt most cells and tissues, denature proteins, and block disulfide reformation. The combination of quick single-step sample preparation with high throughput dual trapping column single analytical column (DTSC) liquid chromatography-mass spectrometry (LC-MS) achieves "Rapid Proteomics" in which the time from sample collection to actionable data is less than 1 hour. The presented development and systematic evaluation of this methodology found reproducible quantitation of over 160 proteins from just 1 microliter of whole blood. Furthermore, the preference of the HTA-protease for intact proteins over peptides allows for sensitive targeted quantitation of the Angiotensin I and II bioactive peptides in under half an hour. With these methods we analyzed serum and plasma from 53 individuals and quantified Angiotensin and proteins that were not detected with trypsin. This assessment of Rapid Proteomics suggests that concentration of circulating protein and peptide biomarkers could be measured in almost real-time by LC-MS. TOC Figure Rapid proteomics enables near real-time monitoring of circulating blood biomarkers. One microliter of blood is collected every 8 minutes, digested for 20 minutes, and then analyzed by targeted mass spectrometry for 8 minutes. This results in a 30-minute delay with datapoints every 8 minutes.
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28
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Shannon AE, Teodorescu RN, Soon N, Heil LR, Jacob CC, Remes PM, Rubinstein MP, Searle BC. A workflow for targeted proteomics assay development using a versatile linear ion trap. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596891. [PMID: 38853838 PMCID: PMC11160733 DOI: 10.1101/2024.05.31.596891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopeDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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29
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Li K, Teo GC, Yang KL, Yu F, Nesvizhskii AI. diaTracer enables spectrum-centric analysis of diaPASEF proteomics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595875. [PMID: 38854051 PMCID: PMC11160675 DOI: 10.1101/2024.05.25.595875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Data-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further improves the quantification accuracy and protein depth achievable using DIA. We introduce diaTracer, a new spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (m/z, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved "pseudo-MS/MS" spectra, facilitating direct ("spectral-library free") peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from cerebrospinal fluid (CSF) and plasma samples, data from phosphoproteomics and HLA immunopeptidomics experiments, and low-input data from a spatial proteomics study. We also show that diaTracer enables unrestricted identification of post-translational modifications from diaPASEF data using open/mass offset searches.
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Affiliation(s)
- Kai Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kevin L. Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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30
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Yazaki J, Yamanashi T, Nemoto S, Kobayashi A, Han YW, Hasegawa T, Iwase A, Ishikawa M, Konno R, Imami K, Kawashima Y, Seita J. Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry. Biol Methods Protoc 2024; 9:bpae039. [PMID: 38884001 PMCID: PMC11180226 DOI: 10.1093/biomethods/bpae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Mapping protein interaction complexes in their natural state in vivo is arguably the Holy Grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe the development of HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assays. As a proof-of-principle, we used HaloMS to evaluate the protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and AI-based prediction tools. Applying HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor (TF)-protein complexes, revealing proteome-wide human adipocyte TF networks and shedding light on how different pathways are integrated.
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Affiliation(s)
- Junshi Yazaki
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Faculty of Agriculture, Laboratory for Genome Biology, Setsunan University, Osaka, 573-0101, Japan
| | - Takashi Yamanashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Shino Nemoto
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Atsuo Kobayashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yong-Woon Han
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Tomoko Hasegawa
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Akira Iwase
- Cell Function Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Ryo Konno
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Jun Seita
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
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31
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Nielsen CPS, Arribas-Hernández L, Han L, Reichel M, Woessmann J, Daucke R, Bressendorff S, López-Márquez D, Andersen SU, Pumplin N, Schoof EM, Brodersen P. Evidence for an RNAi-independent role of Arabidopsis DICER-LIKE2 in growth inhibition and basal antiviral resistance. THE PLANT CELL 2024; 36:2289-2309. [PMID: 38466226 PMCID: PMC11132882 DOI: 10.1093/plcell/koae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 12/13/2023] [Accepted: 01/28/2024] [Indexed: 03/12/2024]
Abstract
Flowering plant genomes encode four or five DICER-LIKE (DCL) enzymes that produce small interfering RNAs (siRNAs) and microRNAs, which function in RNA interference (RNAi). Different RNAi pathways in plants effect transposon silencing, antiviral defense, and endogenous gene regulation. DCL2 acts genetically redundantly with DCL4 to confer basal antiviral defense. However, DCL2 may also counteract DCL4 since knockout of DCL4 causes growth defects that are suppressed by DCL2 inactivation. Current models maintain that RNAi via DCL2-dependent siRNAs is the biochemical basis of both effects. Here, we report that DCL2-mediated antiviral resistance and growth defects cannot be explained by the silencing effects of DCL2-dependent siRNAs. Both functions are defective in genetic backgrounds that maintain high levels of DCL2-dependent siRNAs, either with specific point mutations in DCL2 or with reduced DCL2 dosage because of heterozygosity for dcl2 knockout alleles. Intriguingly, all DCL2 functions require its catalytic activity, and the penetrance of DCL2-dependent growth phenotypes in dcl4 mutants correlates with DCL2 protein levels but not with levels of major DCL2-dependent siRNAs. We discuss this requirement and correlation with catalytic activity but not with resulting siRNAs, in light of other findings that reveal a DCL2 function in innate immunity activation triggered by cytoplasmic double-stranded RNA.
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Affiliation(s)
- Carsten Poul Skou Nielsen
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Laura Arribas-Hernández
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Lijuan Han
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Marlene Reichel
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jakob Woessmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Bygningstorvet, DK-2800 Lyngby, Denmark
| | - Rune Daucke
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Bygningstorvet, DK-2800 Lyngby, Denmark
| | - Simon Bressendorff
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Diego López-Márquez
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Nathan Pumplin
- Swiss Federal Institute of Technology, Institute of Molecular Plant Biology, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Bygningstorvet, DK-2800 Lyngby, Denmark
| | - Peter Brodersen
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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32
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Akshintala VS, Moore M, Cruz-Monserrate Z, Nathan JD, Searle BC, Abu-El-Haija M. Urine Proteomics Profiling Identifies Novel Acute Pancreatitis Diagnostic Biomarkers in a Pediatric Population. Gastroenterology 2024:S0016-5085(24)04937-0. [PMID: 38797238 DOI: 10.1053/j.gastro.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/12/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Affiliation(s)
- Venkata S Akshintala
- Division of Gastroenterology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Madalyn Moore
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Zobeida Cruz-Monserrate
- Division of Gastroenterology, Hepatology and Nutrition and, The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Jaimie D Nathan
- Department of Pediatric Abdominal Transplant and Hepatopancreatobiliary Surgery, Nationwide Children's Hospital, Columbus, Ohio; Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Brian C Searle
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio.
| | - Maisam Abu-El-Haija
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
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33
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Romero Romero ML, Poehls J, Kirilenko A, Richter D, Jumel T, Shevchenko A, Toth-Petroczy A. Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough. Nat Commun 2024; 15:4446. [PMID: 38789441 PMCID: PMC11126739 DOI: 10.1038/s41467-024-48387-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Stop codon readthrough events give rise to longer proteins, which may alter the protein's function, thereby generating short-lasting phenotypic variability from a single gene. In order to systematically assess the frequency and origin of stop codon readthrough events, we designed a library of reporters. We introduced premature stop codons into mScarlet, which enabled high-throughput quantification of protein synthesis termination errors in E. coli using fluorescent microscopy. We found that under stress conditions, stop codon readthrough may occur at rates as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon readthrough events. The analysis of selected reporters by mass spectrometry and RNA-seq showed that not only translation but also transcription errors contribute to stop codon readthrough. The RNA polymerase was more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide detection of stop codon readthrough by mass spectrometry revealed that temperature regulated the expression of cryptic sequences generated by stop codon readthrough in E. coli. Overall, our findings suggest that the environment affects the accuracy of protein production, which increases protein heterogeneity when the organisms need to adapt to new conditions.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Anastasiia Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Tobias Jumel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany.
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34
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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35
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Lu XY, Wu HP, Ma H, Li H, Li J, Liu YT, Pan ZY, Xie Y, Wang L, Ren B, Liu GK. Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives. Anal Chem 2024; 96:7959-7975. [PMID: 38662943 DOI: 10.1021/acs.analchem.4c01639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Spectrum-structure correlation is playing an increasingly crucial role in spectral analysis and has undergone significant development in recent decades. With the advancement of spectrometers, the high-throughput detection triggers the explosive growth of spectral data, and the research extension from small molecules to biomolecules accompanies massive chemical space. Facing the evolving landscape of spectrum-structure correlation, conventional chemometrics becomes ill-equipped, and deep learning assisted chemometrics rapidly emerges as a flourishing approach with superior ability of extracting latent features and making precise predictions. In this review, the molecular and spectral representations and fundamental knowledge of deep learning are first introduced. We then summarize the development of how deep learning assist to establish the correlation between spectrum and molecular structure in the recent 5 years, by empowering spectral prediction (i.e., forward structure-spectrum correlation) and further enabling library matching and de novo molecular generation (i.e., inverse spectrum-structure correlation). Finally, we highlight the most important open issues persisted with corresponding potential solutions. With the fast development of deep learning, it is expected to see ultimate solution of establishing spectrum-structure correlation soon, which would trigger substantial development of various disciplines.
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Affiliation(s)
- Xin-Yu Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Hao-Ping Wu
- State Key Laboratory of Marine Environmental Science, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, P. R. China
| | - Hao Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Hui Li
- Key Laboratory of Multimedia Trusted Perception and Efficient Computing, Ministry of Education of China, Xiamen University, Xiamen 361005, P. R. China
| | - Jia Li
- Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, P. R. China
| | - Yan-Ti Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Zheng-Yan Pan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yi Xie
- School of Informatics, Xiamen University, Xiamen 361005, P. R. China
| | - Lei Wang
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Guo-Kun Liu
- State Key Laboratory of Marine Environmental Science, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, P. R. China
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36
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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37
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Adams C, Gabriel W, Laukens K, Picciani M, Wilhelm M, Bittremieux W, Boonen K. Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF. Nat Commun 2024; 15:3956. [PMID: 38730277 PMCID: PMC11087512 DOI: 10.1038/s41467-024-48322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. We analyze 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project on a timsTOF-Pro to generate a ground-truth dataset containing 93,227 MS/MS spectra of 74,847 unique peptides, that is used to fine-tune the deep learning-based fragment ion intensity prediction model Prosit. We demonstrate up to 3-fold improvement in the identification of immunopeptides, as well as increased detection of immunopeptides from low input samples.
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Affiliation(s)
- Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Wassim Gabriel
- Computational Mass Spectrometry, Technical University of Munich, 85354, Freising, Germany
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Mario Picciani
- Computational Mass Spectrometry, Technical University of Munich, 85354, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich, 85354, Freising, Germany
- Munich Data Science Institute, Technical University of Munich, 85748, Garching, Germany
| | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, Antwerp, Belgium.
| | - Kurt Boonen
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
- Sustainable Health Department, Flemish Institute for Technological Research (VITO), Antwerp, Belgium.
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38
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Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ. A framework for quality control in quantitative proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589318. [PMID: 38645098 PMCID: PMC11030400 DOI: 10.1101/2024.04.12.589318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share real-world case studies applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis using Skyline, longitudinal QC metrics using AutoQC, and server-based data deposition using PanoramaWeb. We propose that this integrated approach to QC be used as a starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible.
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Affiliation(s)
- Kristine A. Tsantilas
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Julia E. Robbins
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Jea Park
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Deanna L. Plubell
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Washington 98195, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Brendan X. MacLean
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Josh Eckels
- LabKey, 500 Union St #1000, Seattle, Washington 98101, United States
| | - Christine C. Wu
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael S. Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27607
| | - Sandra E. Spencer
- Canada’s Michael Smith Genome Sciences Centre (BC Cancer Research Institute), University of British Columbia, Vancouver, British Columbia V5Z 4S6, Canada
| | - Andrew N. Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Washington 98195, United States
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39
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Freestone J, Noble WS, Keich U. Analysis of Tandem Mass Spectrometry Data with CONGA: Combining Open and Narrow Searches with Group-Wise Analysis. J Proteome Res 2024. [PMID: 38652578 DOI: 10.1021/acs.jproteome.3c00399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Searching for tandem mass spectrometry proteomics data against a database is a well-established method for assigning peptide sequences to observed spectra but typically cannot identify peptides harboring unexpected post-translational modifications (PTMs). Open modification searching aims to address this problem by allowing a spectrum to match a peptide even if the spectrum's precursor mass differs from the peptide mass. However, expanding the search space in this way can lead to a loss of statistical power to detect peptides. We therefore developed a method, called CONGA (combining open and narrow searches with group-wise analysis), that takes into account results from both types of searches─a traditional "narrow window" search and an open modification search─while carrying out rigorous false discovery rate control. The result is an algorithm that provides the best of both worlds: the ability to detect unexpected PTMs without a concomitant loss of power to detect unmodified peptides.
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Affiliation(s)
- Jack Freestone
- School of Mathematics and Statistics F07, University of Sydney, NSW 2006, Australia
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Uri Keich
- School of Mathematics and Statistics F07, University of Sydney, NSW 2006, Australia
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40
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Basharat AR, Xiong X, Xu T, Zang Y, Sun L, Liu X. TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588302. [PMID: 38645171 PMCID: PMC11030422 DOI: 10.1101/2024.04.05.588302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Top-down mass spectrometry is widely used for proteoform identification, characterization, and quantification owing to its ability to analyze intact proteoforms. In the last decade, top-down proteomics has been dominated by top-down data-dependent acquisition mass spectrometry (TD-DDA-MS), and top-down data-independent acquisition mass spectrometry (TD-DIA-MS) has not been well studied. While TD-DIA-MS produces complex multiplexed tandem mass spectrometry (MS/MS) spectra, which are challenging to confidently identify, it selects more precursor ions for MS/MS analysis and has the potential to increase proteoform identifications compared with TD-DDA-MS. Here we present TopDIA, the first software tool for proteoform identification by TD-DIA-MS. It generates demultiplexed pseudo MS/MS spectra from TD-DIA-MS data and then searches the pseudo MS/MS spectra against a protein sequence database for proteoform identification. We compared the performance of TD-DDA-MS and TD-DIA-MS using Escherichia coli K-12 MG1655 cells and demonstrated that TD-DIA-MS with TopDIA increased proteoform and protein identifications compared with TD-DDA-MS.
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Affiliation(s)
- Abdul Rehman Basharat
- Department of BioHealth Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Xingzhao Xiong
- Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Tian Xu
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Yong Zang
- Department of Biostatistics and Health Data Sciences, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Xiaowen Liu
- Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA
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41
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Villacrés C, Mizero B, Spicer V, Viner R, Saba J, Patel B, Snovida S, Jensen P, Huhmer A, Krokhin OV. Toward an Ultimate Solution for Peptide Retention Time Prediction: The Effect of Column Temperature on Separation Selectivity. J Proteome Res 2024; 23:1488-1494. [PMID: 38530092 DOI: 10.1021/acs.jproteome.4c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
We studied the effect of the column temperature on the selectivity of reversed-phase peptide separation in bottom-up proteomics. The number of peptide identifications from 2 h liquid chromatography with tandem mass spectrometry (LC-MS/MS) acquisitions reaches a plateau at 45-55 °C, driven simultaneously by improved separation efficiency, a gradual decrease in peptide retention, and possible on-column degradation of peptides at elevated temperatures. Performing 2D LC-MS/MS acquisitions at 25, 35, 45, and 55 °C resulted in the identification of ∼100,000 and ∼120,000 unique peptides for nonmodified and tandem mass tags (TMT)-labeled samples, respectively. These peptide collections were used to investigate the temperature-driven retention features. The latter is governed by the specific temperature response of individual residues, peptide hydrophobicity and length, and amphipathic helicity. On average, peptide retention decreased by 0.56 and 0.5% acetonitrile for each 10 °C increase for label-free and TMT-labeled peptides, respectively. This generally linear response of retention shifts allowed the extrapolation of predictive models beyond the studied temperature range. Thus, (trap) column cooling from room temperature to 0 °C will allow the retention of an additional 3% of detectable tryptic peptides. Meanwhile, the application of 90 °C would result in the loss of ∼20% of tryptic peptides that were amenable to MS/MS-based identification.
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Affiliation(s)
- Carina Villacrés
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada
| | - Benilde Mizero
- Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Julian Saba
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Sergei Snovida
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Penny Jensen
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Andreas Huhmer
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada
- Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg R3E 3P4, Canada
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42
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Peng J, Svetec N, Molina H, Zhao L. The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions. Mol Biol Evol 2024; 41:msae065. [PMID: 38518286 PMCID: PMC11017328 DOI: 10.1093/molbev/msae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/22/2024] [Accepted: 03/18/2024] [Indexed: 03/24/2024] Open
Abstract
Post-mating responses play a vital role in successful reproduction across diverse species. In fruit flies, sex peptide binds to the sex peptide receptor, triggering a series of post-mating responses. However, the origin of sex peptide receptor predates the emergence of sex peptide. The evolutionary origins of the interactions between sex peptide and sex peptide receptor and the mechanisms by which they interact remain enigmatic. In this study, we used ancestral sequence reconstruction, AlphaFold2 predictions, and molecular dynamics simulations to study sex peptide-sex peptide receptor interactions and their origination. Using AlphaFold2 and long-time molecular dynamics simulations, we predicted the structure and dynamics of sex peptide-sex peptide receptor interactions. We show that sex peptide potentially binds to the ancestral states of Diptera sex peptide receptor. Notably, we found that only a few amino acid changes in sex peptide receptor are sufficient for the formation of sex peptide-sex peptide receptor interactions. Ancestral sequence reconstruction and molecular dynamics simulations further reveal that sex peptide receptor interacts with sex peptide through residues that are mostly involved in the interaction interface of an ancestral ligand, myoinhibitory peptides. We propose a potential mechanism whereby sex peptide-sex peptide receptor interactions arise from the preexisting myoinhibitory peptides-sex peptide receptor interface as well as early chance events both inside and outside the preexisting interface that created novel sex peptide-specific sex peptide-sex peptide receptor interactions. Our findings provide new insights into the origin and evolution of sex peptide-sex peptide receptor interactions and their relationship with myoinhibitory peptides-sex peptide receptor interactions.
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Affiliation(s)
- Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
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43
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Choi S, Paek E. pXg: Comprehensive Identification of Noncanonical MHC-I-Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads. Mol Cell Proteomics 2024; 23:100743. [PMID: 38403075 PMCID: PMC10979277 DOI: 10.1016/j.mcpro.2024.100743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024] Open
Abstract
Discovering noncanonical peptides has been a common application of proteogenomics. Recent studies suggest that certain noncanonical peptides, known as noncanonical major histocompatibility complex-I (MHC-I)-associated peptides (ncMAPs), that bind to MHC-I may make good immunotherapeutic targets. De novo peptide sequencing is a great way to find ncMAPs since it can detect peptide sequences from their tandem mass spectra without using any sequence databases. However, this strategy has not been widely applied for ncMAP identification because there is not a good way to estimate its false-positive rates. In order to completely and accurately identify immunopeptides using de novo peptide sequencing, we describe a unique pipeline called proteomics X genomics. In contrast to current pipelines, it makes use of genomic data, RNA-Seq abundance and sequencing quality, in addition to proteomic features to increase the sensitivity and specificity of peptide identification. We show that the peptide-spectrum match quality and genetic traits have a clear relationship, showing that they can be utilized to evaluate peptide-spectrum matches. From 10 samples, we found 24,449 canonical MHC-I-associated peptides and 956 ncMAPs by using a target-decoy competition. Three hundred eighty-seven ncMAPs and 1611 canonical MHC-I-associated peptides were new identifications that had not yet been published. We discovered 11 ncMAPs produced from a squirrel monkey retrovirus in human cell lines in addition to the two ncMAPs originating from a complementarity determining region 3 in an antibody thanks to the unrestricted search space assumed by de novo sequencing. These entirely new identifications show that proteomics X genomics can make the most of de novo peptide sequencing's advantages and its potential use in the search for new immunotherapeutic targets.
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Affiliation(s)
- Seunghyuk Choi
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea
| | - Eunok Paek
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea; Institute for Artificial Intelligence Research, Hanyang University, Seoul, Republic of Korea.
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44
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Korchak JA, Jeffery ED, Bandyopadhyay S, Jordan BT, Lehe M, Watts EF, Fenix A, Wilhelm M, Sheynkman GM. IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587549. [PMID: 38617311 PMCID: PMC11014528 DOI: 10.1101/2024.04.01.587549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Alternative splicing is a major contributor of transcriptomic complexity, but the extent to which transcript isoforms are translated into stable, functional protein isoforms is unclear. Furthermore, detection of relatively scarce isoform-specific peptides is challenging, with many protein isoforms remaining uncharted due to technical limitations. Recently, a family of advanced targeted MS strategies, termed internal standard parallel reaction monitoring (IS-PRM), have demonstrated multiplexed, sensitive detection of pre-defined peptides of interest. Such approaches have not yet been used to confirm existence of novel peptides. Here, we present a targeted proteogenomic approach that leverages sample-matched long-read RNA sequencing (LR RNAseq) data to predict potential protein isoforms with prior transcript evidence. Predicted tryptic isoform-specific peptides, which are specific to individual gene product isoforms, serve as "triggers" and "targets" in the IS-PRM method, Tomahto. Using the model human stem cell line WTC11, LR RNAseq data were generated and used to inform the generation of synthetic standards for 192 isoform-specific peptides (114 isoforms from 55 genes). These synthetic "trigger" peptides were labeled with super heavy tandem mass tags (TMT) and spiked into TMT-labeled WTC11 tryptic digest, predicted to contain corresponding endogenous "target" peptides. Compared to DDA mode, Tomahto increased detectability of isoforms by 3.6-fold, resulting in the identification of five previously unannotated isoforms. Our method detected protein isoform expression for 43 out of 55 genes corresponding to 54 resolved isoforms. This LR RNA seq-informed Tomahto targeted approach, called LRP-IS-PRM, is a new modality for generating protein-level evidence of alternative isoforms - a critical first step in designing functional studies and eventually clinical assays.
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Affiliation(s)
- Jennifer A. Korchak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Erin D. Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Saikat Bandyopadhyay
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ben T. Jordan
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Micah Lehe
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Emily F. Watts
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Aidan Fenix
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA
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45
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Adams C, Laukens K, Bittremieux W, Boonen K. Machine learning-based peptide-spectrum match rescoring opens up the immunopeptidome. Proteomics 2024; 24:e2300336. [PMID: 38009585 DOI: 10.1002/pmic.202300336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/29/2023]
Abstract
Immunopeptidomics is a key technology in the discovery of targets for immunotherapy and vaccine development. However, identifying immunopeptides remains challenging due to their non-tryptic nature, which results in distinct spectral characteristics. Moreover, the absence of strict digestion rules leads to extensive search spaces, further amplified by the incorporation of somatic mutations, pathogen genomes, unannotated open reading frames, and post-translational modifications. This inflation in search space leads to an increase in random high-scoring matches, resulting in fewer identifications at a given false discovery rate. Peptide-spectrum match rescoring has emerged as a machine learning-based solution to address challenges in mass spectrometry-based immunopeptidomics data analysis. It involves post-processing unfiltered spectrum annotations to better distinguish between correct and incorrect peptide-spectrum matches. Recently, features based on predicted peptidoform properties, including fragment ion intensities, retention time, and collisional cross section, have been used to improve the accuracy and sensitivity of immunopeptide identification. In this review, we describe the diverse bioinformatics pipelines that are currently available for peptide-spectrum match rescoring and discuss how they can be used for the analysis of immunopeptidomics data. Finally, we provide insights into current and future machine learning solutions to boost immunopeptide identification.
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Affiliation(s)
- Charlotte Adams
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Laboratory of Protein Science, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Wout Bittremieux
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Laboratory of Protein Science, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- ImmuneSpec BV, Niel, Belgium
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46
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Zhu C, Liu LY, Yamaguchi TN, Zhu H, Hugh-White R, Livingstone J, Patel Y, Kislinger T, Boutros PC. moPepGen: Rapid and Comprehensive Proteoform Identification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587261. [PMID: 38585946 PMCID: PMC10996593 DOI: 10.1101/2024.03.28.587261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Gene expression is a multi-step transformation of biological information from its storage form (DNA) into functional forms (protein and some RNAs). Regulatory activities at each step of this transformation multiply a single gene into a myriad of proteoforms. Proteogenomics is the study of how genomic and transcriptomic variation creates this proteoform diversity, and is limited by the challenges of modeling the complexities of gene-expression. We therefore created moPepGen, a graph-based algorithm that comprehensively enumerates proteoforms in linear time. moPepGen works with multiple technologies, in multiple species and on all types of genetic and transcriptomic data. In human cancer proteomes, it detects and quantifies previously unobserved noncanonical peptides arising from germline and somatic genomic variants, noncoding open reading frames, RNA fusions and RNA circularization. By enabling efficient identification and quantitation of previously hidden proteins in both existing and new proteomic data, moPepGen facilitates all proteogenomics applications. It is available at: https://github.com/uclahs-cds/package-moPepGen.
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Affiliation(s)
- Chenghao Zhu
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, CA, USA
- Department of Urology, University of California, Los Angeles, CA, USA
| | - Lydia Y. Liu
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Vector Institute for Artificial Intelligence, Toronto, Canada
| | - Takafumi N. Yamaguchi
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, CA, USA
| | - Helen Zhu
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Vector Institute for Artificial Intelligence, Toronto, Canada
| | - Rupert Hugh-White
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, CA, USA
| | - Julie Livingstone
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, CA, USA
| | - Yash Patel
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, CA, USA
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Paul C. Boutros
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, CA, USA
- Department of Urology, University of California, Los Angeles, CA, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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47
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Nayak D, Lv D, Yuan Y, Zhang P, Hu W, Nayak A, Ruben EA, Lv Z, Sung P, Hromas R, Zheng G, Zhou D, Olsen SK. Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL. Nat Commun 2024; 15:2743. [PMID: 38548768 PMCID: PMC10979003 DOI: 10.1038/s41467-024-46922-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Overexpression of BCL-xL and BCL-2 play key roles in tumorigenesis and cancer drug resistance. Advances in PROTAC technology facilitated recent development of the first BCL-xL/BCL-2 dual degrader, 753b, a VHL-based degrader with improved potency and reduced toxicity compared to previous small molecule inhibitors. Here, we determine crystal structures of VHL/753b/BCL-xL and VHL/753b/BCL-2 ternary complexes. The two ternary complexes exhibit markedly different architectures that are accompanied by distinct networks of interactions at the VHL/753b-linker/target interfaces. The importance of these interfacial contacts is validated via functional analysis and informed subsequent rational and structure-guided design focused on the 753b linker and BCL-2/BCL-xL warhead. This results in the design of a degrader, WH244, with enhanced potency to degrade BCL-xL/BCL-2 in cells. Using biophysical assays followed by in cell activities, we are able to explain the enhanced target degradation of BCL-xL/BCL-2 in cells. Most PROTACs are empirically designed and lack structural studies, making it challenging to understand their modes of action and specificity. Our work presents a streamlined approach that combines rational design and structure-based insights backed with cell-based studies to develop effective PROTAC-based cancer therapeutics.
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Affiliation(s)
- Digant Nayak
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Dongwen Lv
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Yaxia Yuan
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Peiyi Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Wanyi Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Anindita Nayak
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Eliza A Ruben
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Zongyang Lv
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Patrick Sung
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Robert Hromas
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
| | - Daohong Zhou
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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48
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Gunter HM, Youlten SE, Reis ALM, McCubbin T, Madala BS, Wong T, Stevanovski I, Cipponi A, Deveson IW, Santini NS, Kummerfeld S, Croucher PI, Marcellin E, Mercer TR. A universal molecular control for DNA, mRNA and protein expression. Nat Commun 2024; 15:2480. [PMID: 38509097 PMCID: PMC10954659 DOI: 10.1038/s41467-024-46456-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.
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Affiliation(s)
- Helen M Gunter
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott E Youlten
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Andre L M Reis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Tim McCubbin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Bindu Swapna Madala
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Ted Wong
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
| | - Arcadi Cipponi
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, New South Wales, Australia
- School of Electrical and Information Engineering, University of Sydney, Sydney, New South Wales, Australia
| | - Nadia S Santini
- Centro Nacional de Investigación Disciplinaria en Conservación y Mejoramiento de Ecosistemas Forestales, INIFAP, Ciudad de México, 04010, Mexico
| | - Sarah Kummerfeld
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter I Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Esteban Marcellin
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Tim R Mercer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.
- BASE mRNA Facility, The University of Queensland, Brisbane, Queensland, Australia.
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Brisbane, Queensland, Australia.
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
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49
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Yang Y, Fang Q. Prediction of glycopeptide fragment mass spectra by deep learning. Nat Commun 2024; 15:2448. [PMID: 38503734 PMCID: PMC10951270 DOI: 10.1038/s41467-024-46771-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Deep learning has achieved a notable success in mass spectrometry-based proteomics and is now emerging in glycoproteomics. While various deep learning models can predict fragment mass spectra of peptides with good accuracy, they cannot cope with the non-linear glycan structure in an intact glycopeptide. Herein, we present DeepGlyco, a deep learning-based approach for the prediction of fragment spectra of intact glycopeptides. Our model adopts tree-structured long-short term memory networks to process the glycan moiety and a graph neural network architecture to incorporate potential fragmentation pathways of a specific glycan structure. This feature is beneficial to model explainability and differentiation ability of glycan structural isomers. We further demonstrate that predicted spectral libraries can be used for data-independent acquisition glycoproteomics as a supplement for library completeness. We expect that this work will provide a valuable deep learning resource for glycoproteomics.
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Affiliation(s)
- Yi Yang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
| | - Qun Fang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China.
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50
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Rios KT, McGee JP, Sebastian A, Moritz RL, Feric M, Absalon S, Swearingen KE, Lindner SE. Global Release of Translational Repression Across Plasmodium's Host-to-Vector Transmission Event. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577866. [PMID: 38352447 PMCID: PMC10862809 DOI: 10.1101/2024.02.01.577866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Malaria parasites must be able to respond quickly to changes in their environment, including during their transmission between mammalian hosts and mosquito vectors. Therefore, before transmission, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. This essential regulatory control requires the orthologues of DDX6 (DOZI), LSM14a (CITH), and ALBA proteins to form a translationally repressive complex in female gametocytes that associates with many of the affected mRNAs. However, while the release of translational repression of individual mRNAs has been documented, the details of the global release of translational repression have not. Moreover, the changes in spatial arrangement and composition of the DOZI/CITH/ALBA complex that contribute to translational control are also not known. Therefore, we have conducted the first quantitative, comparative transcriptomics and DIA-MS proteomics of Plasmodium parasites across the host-to-vector transmission event to document the global release of translational repression. Using female gametocytes and zygotes of P. yoelii, we found that nearly 200 transcripts are released for translation soon after fertilization, including those with essential functions for the zygote. However, we also observed that some transcripts remain repressed beyond this point. In addition, we have used TurboID-based proximity proteomics to interrogate the spatial and compositional changes in the DOZI/CITH/ALBA complex across this transmission event. Consistent with recent models of translational control, proteins that associate with either the 5' or 3' end of mRNAs are in close proximity to one another during translational repression in female gametocytes and then dissociate upon release of repression in zygotes. This observation is cross-validated for several protein colocalizations in female gametocytes via ultrastructure expansion microscopy and structured illumination microscopy. Moreover, DOZI exchanges its interaction from NOT1-G in female gametocytes to the canonical NOT1 in zygotes, providing a model for a trigger for the release of mRNAs from DOZI. Finally, unenriched phosphoproteomics revealed the modification of key translational control proteins in the zygote. Together, these data provide a model for the essential translational control mechanisms used by malaria parasites to promote their efficient transmission from their mammalian host to their mosquito vector.
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Affiliation(s)
- Kelly T. Rios
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
| | - James P. McGee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802
| | | | - Marina Feric
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Sabrina Absalon
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202
| | | | - Scott E. Lindner
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
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