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Wang Q, Gao G, Fang F, Wang Q, Lundquist PK, Sun L. A simple and efficient approach for preparing cationic coating with tunable electroosmotic flow for capillary zone electrophoresis-mass spectrometry-based top-down proteomics. Anal Chim Acta 2024; 1328:343162. [PMID: 39266194 PMCID: PMC11404064 DOI: 10.1016/j.aca.2024.343162] [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: 06/12/2024] [Revised: 08/20/2024] [Accepted: 08/26/2024] [Indexed: 09/14/2024]
Abstract
BACKGROUND Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has become a valuable analytical technique in top-down proteomics (TDP). CZE-MS/MS-based TDP typically employs separation capillaries with neutral coatings (i.e., linear polyacrylamide, LPA). However, issues related to separation resolution and reproducibility remain with the LPA-coated capillaries due to the unavoidable non-specific protein adsorption onto the capillary wall. Cationic coatings can be critical alternatives to LPA coating for CZE-MS/MS-based TDP due to the electrostatic repulsion between the positively charged capillary inner wall and proteoform molecules in the acidic separation buffer. Unfortunately, there are only very few studies using cationic coating-based CZE-MS/MS for TDP studies. RESULTS In this work, we aimed to develop a simple and efficient approach for preparing separation capillaries with a cationic coating, i.e., poly (acrylamide-co-(3-acrylamidopropyl) trimethylammonium chloride [PAMAPTAC]) for CZE-MS/MS-based TDP. The PAMAPTAC coating-based CZE-MS produced significantly better separation resolution of proteoforms compared to the traditionally used LPA-coated approach. It achieved reproducible separation and measurement of a simple proteoform mixture and a complex proteome sample (i.e., a yeast cell lysate) regarding migration time, proteoform intensity, and the number of proteoform identifications. The PAMAPTAC coating-based CZE-MS enabled the detection of large proteoforms (≥30 kDa) from the yeast cell lysate reproducibly without any size-based prefractionation. Interestingly, the mobility of proteoforms using the PAMAPTAC coating can be predicted accurately using a simple semi-empirical model. SIGNIFICANCE The results render the PAMAPTAC coating as a valuable alternative to the LPA coating to advance CZE-MS-based TDP towards high-resolution separation and highly reproducible measurement of proteoforms in complex samples.
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Affiliation(s)
- Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Guangyao Gao
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Peter K Lundquist
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA.
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2
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Wang CR, Zenaidee MA, Snel MF, Pukala TL. Exploring Top-Down Mass Spectrometric Approaches To Probe Forest Cobra ( Naja melanoleuca) Venom Proteoforms. J Proteome Res 2024; 23:4601-4613. [PMID: 39231368 DOI: 10.1021/acs.jproteome.4c00486] [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: 09/06/2024]
Abstract
Snake venoms are comprised of bioactive proteins and peptides that facilitate severe snakebite envenomation symptoms. A comprehensive understanding of venom compositions and the subtle heterogeneity therein is important. While bottom-up proteomics has been the well-established approach to catalogue venom compositions, top-down proteomics has emerged as a complementary strategy to characterize venom heterogeneity at the intact protein level. However, top-down proteomics has not been as widely implemented in the snake venom field as bottom-up proteomics, with various emerging top-down methods yet to be developed for venom systems. Here, we have explored three main top-down mass spectrometry methodologies in a proof-of-concept study to characterize selected three-finger toxin and phospholipase A2 proteoforms from the forest cobra (Naja melanoleuca) venom. We demonstrated the utility of a data-independent acquisition mode "MSE" for untargeted fragmentation on a chromatographic time scale and its improvement in protein sequence coverage compared to conventional targeted tandem mass spectrometry analysis. We also showed that protein identification can be further improved using a hybrid fragmentation approach, combining electron-capture dissociation and collision-induced dissociation. Lastly, we reported the promising application of multifunctional cyclic ion mobility separation and post-ion mobility fragmentation on snake venom proteins for the first time.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Muhammad A Zenaidee
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Marten F Snel
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Proteomics, Metabolomics and MS-Imaging Core Facility, South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
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3
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Huang CF, Hollas MA, Sanchez A, Bhattacharya M, Ho G, Sundaresan A, Caldwell MA, Zhao X, Benz R, Siddiqui A, Kelleher NL. Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-Down Proteomics. J Proteome Res 2024; 23:4694-4703. [PMID: 39312774 DOI: 10.1021/acs.jproteome.4c00621] [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: 09/25/2024]
Abstract
The dynamic range challenge for the detection of proteins and their proteoforms in human plasma has been well documented. Here, we use the nanoparticle protein corona approach to enrich low-abundance proteins selectively and reproducibly from human plasma and use top-down proteomics to quantify differential enrichment for the 2841 detected proteoforms from 114 proteins. Furthermore, nanoparticle enrichment allowed top-down detection of proteoforms between ∼1 μg/mL and ∼10 pg/mL in absolute abundance, providing up to a 105-fold increase in proteome depth over neat plasma in which only proteoforms from abundant proteins (>1 μg/mL) were detected. The ability to monitor medium and some low-abundant proteoforms through reproducible enrichment significantly extends the applicability of proteoform research by adding depth beyond albumin, immunoglobins, and apolipoproteins to uncover many involved in immunity and cell signaling. As proteoforms carry unique information content relative to peptides, this report opens the door to deeper proteoform sequencing in clinical proteomics of disease or aging cohorts.
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Affiliation(s)
- Che-Fan Huang
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael A Hollas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Aniel Sanchez
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | | | - Giang Ho
- Seer Inc., Redwood City, California 94065, United States
| | | | - Michael A Caldwell
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Xiaoyan Zhao
- Seer Inc., Redwood City, California 94065, United States
| | - Ryan Benz
- Seer Inc., Redwood City, California 94065, United States
| | - Asim Siddiqui
- Seer Inc., Redwood City, California 94065, United States
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
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4
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Chakrabarty S, Wang S, Roychowdhury T, Ginsberg SD, Chiosis G. Introducing dysfunctional Protein-Protein Interactome (dfPPI) - A platform for systems-level protein-protein interaction (PPI) dysfunction investigation in disease. Curr Opin Struct Biol 2024; 88:102886. [PMID: 39003916 PMCID: PMC11392609 DOI: 10.1016/j.sbi.2024.102886] [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: 05/05/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024]
Abstract
Protein-protein interactions (PPIs) play a crucial role in cellular function and disease manifestation, with dysfunctions in PPI networks providing a direct link between stressors and phenotype. The dysfunctional Protein-Protein Interactome (dfPPI) platform, formerly known as epichaperomics, is a newly developed chemoproteomic method aimed at detecting dynamic changes at the systems level in PPI networks under stressor-induced cellular perturbations within disease states. This review provides an overview of dfPPIs, emphasizing the novel methodology, data analytics, and applications in disease research. dfPPI has applications in cancer research, where it identifies dysfunctions integral to maintaining malignant phenotypes and discovers strategies to enhance the efficacy of current therapies. In neurodegenerative disorders, dfPPI uncovers critical dysfunctions in cellular processes and stressor-specific vulnerabilities. Challenges, including data complexity and the potential for integration with other omics datasets are discussed. The dfPPI platform is a potent tool for dissecting disease systems biology by directly informing on dysfunctions in PPI networks and holds promise for advancing disease identification and therapeutics.
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Affiliation(s)
- Souparna Chakrabarty
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Shujuan Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Tanaya Roychowdhury
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Stephen D Ginsberg
- Departments of Psychiatry, Neuroscience & Physiology & the NYU Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA; Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, 10962, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA; Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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5
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Kjer-Hansen P, Phan TG, Weatheritt RJ. Protein isoform-centric therapeutics: expanding targets and increasing specificity. Nat Rev Drug Discov 2024; 23:759-779. [PMID: 39232238 DOI: 10.1038/s41573-024-01025-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
Most protein-coding genes produce multiple protein isoforms; however, these isoforms are commonly neglected in drug discovery. The expression of protein isoforms can be specific to a disease, tissue and/or developmental stage, and this specific expression can be harnessed to achieve greater drug specificity than pan-targeting of all gene products and to enable improved treatments for diseases caused by aberrant protein isoform production. In recent years, several protein isoform-centric therapeutics have been developed. Here, we collate these studies and clinical trials to highlight three distinct but overlapping modes of action for protein isoform-centric drugs: isoform switching, isoform introduction or depletion, and modulation of isoform activity. In addition, we discuss how protein isoforms can be used clinically as targets for cell type-specific drug delivery and immunotherapy, diagnostic biomarkers and sources of cancer neoantigens. Collectively, we emphasize the value of a focus on isoforms as a route to discovering drugs with greater specificity and fewer adverse effects. This approach could enable the targeting of proteins for which pan-inhibition of all isoforms is toxic and poorly tolerated.
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Affiliation(s)
- Peter Kjer-Hansen
- EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.
- St. Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, New South Wales, Australia.
| | - Tri Giang Phan
- St. Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, New South Wales, Australia
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Robert J Weatheritt
- EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Núñez E, Gómez-Serrano M, Calvo E, Bonzon-Kulichenko E, Trevisan-Herraz M, Rodríguez JM, García-Marqués F, Magni R, Lara-Pezzi E, Martín-Ventura JL, Camafeita E, Vázquez J. A Multiplexed Quantitative Proteomics Approach to the Human Plasma Protein Signature. Biomedicines 2024; 12:2118. [PMID: 39335631 PMCID: PMC11428418 DOI: 10.3390/biomedicines12092118] [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: 07/22/2024] [Revised: 08/30/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Despite the plasma proteome being able to provide a unique insight into the health and disease status of individuals, holding singular promise as a source of protein biomarkers that could be pivotal in the context of personalized medicine, only around 100 proteins covering a few human conditions have been approved as biomarkers by the US Food and Drug Administration (FDA) so far. Mass spectrometry (MS) currently has enormous potential for high-throughput analysis in clinical research; however, plasma proteomics remains challenging mainly due to the wide dynamic range of plasma protein abundances and the time-consuming procedures required. We applied a new MS-based multiplexed proteomics workflow to quantitate proteins, encompassing 67 FDA-approved biomarkers, in >1300 human plasma samples from a clinical cohort. Our results indicate that this workflow is suitable for large-scale clinical studies, showing good accuracy and reproducibility (coefficient of variation (CV) < 20 for 90% of the proteins). Furthermore, we identified plasma signature proteins (stable in time on an individual basis), stable proteins (exhibiting low biological variability and high temporal stability), and highly variable proteins (with low temporal stability) that can be used for personalized health monitoring and medicine.
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Affiliation(s)
- Estefanía Núñez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - María Gómez-Serrano
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany;
| | - Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - Elena Bonzon-Kulichenko
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
| | - Marco Trevisan-Herraz
- International Center for Life, Newcastle University, Newcastle upon Tyne NE1 4EP, UK;
| | - José Manuel Rodríguez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
| | | | - Ricardo Magni
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - José Luis Martín-Ventura
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
- IIS-Fundación Jiménez-Díaz, 28015 Madrid, Spain
| | - Emilio Camafeita
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
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7
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Sadeghi S, Ashkarran AA, Wang Q, Zhu G, Mahmoudi M, Sun L. Mass Spectrometry-Based Top-Down Proteomics in Nanomedicine: Proteoform-Specific Measurement of Protein Corona. ACS NANO 2024; 18. [PMID: 39276099 PMCID: PMC11440641 DOI: 10.1021/acsnano.4c04675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/30/2024] [Accepted: 09/06/2024] [Indexed: 09/16/2024]
Abstract
Conventional mass spectrometry (MS)-based bottom-up proteomics (BUP) analysis of the protein corona [i.e., an evolving layer of biomolecules, mostly proteins, formed on the surface of nanoparticles (NPs) during their interactions with biomolecular fluids] enabled the nanomedicine community to partly identify the biological identity of NPs. Such an approach, however, fails to pinpoint the specific proteoforms─distinct molecular variants of proteins in the protein corona. The proteoform-level information could potentially advance the prediction of the biological fate and pharmacokinetics of nanomedicines. Recognizing this limitation, this study pioneers a robust and reproducible MS-based top-down proteomics (TDP) technique for characterizing proteoforms in the protein corona. Our TDP approach has successfully identified about 900 proteoforms in the protein corona of polystyrene NPs, ranging from 2 to 70 kDa, revealing proteoforms of 48 protein biomarkers with combinations of post-translational modifications, signal peptide cleavages, and/or truncations─details that BUP could not fully discern. This advancement in MS-based TDP offers a more advanced approach to characterize NP protein coronas, deepening our understanding of NPs' biological identities. We, therefore, propose using both TDP and BUP strategies to obtain more comprehensive information about the protein corona, which, in turn, can further enhance the diagnostic and therapeutic efficacy of nanomedicine technologies.
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Affiliation(s)
- Seyed
Amirhossein Sadeghi
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Ali Akbar Ashkarran
- Department
of Radiology and Precision Health Program, Michigan State University, East Lansing, Michigan 48824, United States
| | - Qianyi Wang
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Guijie Zhu
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Morteza Mahmoudi
- Department
of Radiology and Precision Health Program, Michigan State University, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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8
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Kiseleva OI, Arzumanian VA, Kurbatov IY, Poverennaya EV. In silico and in cellulo approaches for functional annotation of human protein splice variants. BIOMEDITSINSKAIA KHIMIIA 2024; 70:315-328. [PMID: 39324196 DOI: 10.18097/pbmc20247005315] [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: 09/27/2024]
Abstract
The elegance of pre-mRNA splicing mechanisms continues to interest scientists even after over a half century, since the discovery of the fact that coding regions in genes are interrupted by non-coding sequences. The vast majority of human genes have several mRNA variants, coding structurally and functionally different protein isoforms in a tissue-specific manner and with a linkage to specific developmental stages of the organism. Alteration of splicing patterns shifts the balance of functionally distinct proteins in living systems, distorts normal molecular pathways, and may trigger the onset and progression of various pathologies. Over the past two decades, numerous studies have been conducted in various life sciences disciplines to deepen our understanding of splicing mechanisms and the extent of their impact on the functioning of living systems. This review aims to summarize experimental and computational approaches used to elucidate the functions of splice variants of a single gene based on our experience accumulated in the laboratory of interactomics of proteoforms at the Institute of Biomedical Chemistry (IBMC) and best global practices.
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Affiliation(s)
- O I Kiseleva
- Institute of Biomedical Chemistry, Moscow, Russia
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9
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Cobley JN. Exploring the unmapped cysteine redox proteoform landscape. Am J Physiol Cell Physiol 2024; 327:C844-C866. [PMID: 39099422 DOI: 10.1152/ajpcell.00152.2024] [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: 03/07/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 08/06/2024]
Abstract
Cysteine redox proteoforms define the diverse molecular states that proteins with cysteine residues can adopt. A protein with one cysteine residue must adopt one of two binary proteoforms: reduced or oxidized. Their numbers scale: a protein with 10 cysteine residues must assume one of 1,024 proteoforms. Although they play pivotal biological roles, the vast cysteine redox proteoform landscape comprising vast numbers of theoretical proteoforms remains largely uncharted. Progress is hampered by a general underappreciation of cysteine redox proteoforms, their intricate complexity, and the formidable challenges that they pose to existing methods. The present review advances cysteine redox proteoform theory, scrutinizes methodological barriers, and elaborates innovative technologies for detecting unique residue-defined cysteine redox proteoforms. For example, chemistry-enabled hybrid approaches combining the strengths of top-down mass spectrometry (TD-MS) and bottom-up mass spectrometry (BU-MS) for systematically cataloguing cysteine redox proteoforms are delineated. These methods provide the technological means to map uncharted redox terrain. To unravel hidden redox regulatory mechanisms, discover new biomarkers, and pinpoint therapeutic targets by mining the theoretical cysteine redox proteoform space, a community-wide initiative termed the "Human Cysteine Redox Proteoform Project" is proposed. Exploring the cysteine redox proteoform landscape could transform current understanding of redox biology.
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Affiliation(s)
- James N Cobley
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
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10
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Calvete JJ, Lomonte B, Saviola AJ, Calderón Celis F, Ruiz Encinar J. Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives. MASS SPECTROMETRY REVIEWS 2024; 43:977-997. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/24/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.
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Affiliation(s)
- Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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11
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Steinbach MK, Leipert J, Matzanke T, Tholey A. Digital Microfluidics for Sample Preparation in Low-Input Proteomics. SMALL METHODS 2024:e2400495. [PMID: 39205538 DOI: 10.1002/smtd.202400495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Low-input proteomics, also referred to as micro- or nanoproteomics, has become increasingly popular as it allows one to elucidate molecular processes in rare biological materials. A major prerequisite for the analytics of minute protein amounts, e.g., derived from low cell numbers, down to single cells, is the availability of efficient sample preparation methods. Digital microfluidics (DMF), a technology allowing the handling and manipulation of low liquid volumes, has recently been shown to be a powerful and versatile tool to address the challenges in low-input proteomics. Here, an overview is provided on recent advances in proteomics sample preparation using DMF. In particular, the capability of DMF to isolate proteomes from cells and small model organisms, and to perform all necessary chemical sample preparation steps, such as protein denaturation and proteolytic digestion on-chip, are highlighted. Additionally, major prerequisites to making these steps compatible with follow-up analytical methods such as liquid chromatography-mass spectrometry will be discussed.
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Affiliation(s)
- Max K Steinbach
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Jan Leipert
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Theo Matzanke
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
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12
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Wang CR, McFarlane LO, Pukala TL. Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions. Toxicon 2024; 247:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [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: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomic workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Lewis O McFarlane
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia.
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13
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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14
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Zhong J, Song X, Wang S. FREE: Enhanced Feature Representation for Isotopic Envelope Evaluation in Top-Down Mass Spectra Deconvolution. Anal Chem 2024; 96:12602-12615. [PMID: 39037184 DOI: 10.1021/acs.analchem.4c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
The aim of deconvolution of top-down mass spectra is to recognize monoisotopic peaks from the experimental envelopes in raw mass spectra. So accurate assessment of similarity between theoretical and experimental envelopes is a critical step in mass spectra data deconvolution. Existing evaluation methods primarily rely on intensity differences and m/z similarity, potentially lacking a comprehensive assessment. To overcome this constraint and facilitate a comprehensive and refined assessment of the similarity between theoretical and experimental envelopes, there exists an imperative to systematically explore and identify increasingly efficacious features for assessing this correspondence. We present enhanced feature representation for isotopic envelope evaluation (FREE) that derives diverse feature representations, encapsulating fundamental physical attributes of envelopes, including peak intensity and envelope shape. We trained FREE and evaluated its performance on both the ovarian tumor (OT) (human OT cells) data set and zebrafish (ZF) (brain in mature female ZF) data set. Specifically, comparing the state-of-art method, FREE demonstrates higher performance in multiple evaluation metrics across both the OT and ZF data sets, with a particular emphasis on precision, and it demonstrates accurate predictions of a greater number of positive envelopes among the top-ranked envelopes based on their scores. Moreover, within a cross-species data set of ZF, FREE identified a higher number of proteoform-spectrum matches (PrSMs), increasing the count from 50,795 to 52,927 compared to EnvCNN, the amalgamation of FREE with TopFD also exhibits a commendable capacity to discern 117,883 fragment ions, thus surpassing the 97,554 fragment ions identified through the application of EnvCNN in conjunction with TopFD. To further validate the performance of FREE, we have tested 10 a cross-species top-down proteomes containing 36 subdata set from ProteomeXchange. The results reveal that, after deconvolution with TopFD + FREE, TopPIC identifies more PrSMs across these 10 data sets in both the first and second rounds of experiments. These findings underscore the robustness and generalization capabilities of the FREE approach in diverse proteomes.
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Affiliation(s)
- Jiancheng Zhong
- College of Information Science and Engineering, Hunan Normal University, ChangSha 410081, China
| | - Xingran Song
- College of Information Science and Engineering, Hunan Normal University, ChangSha 410081, China
| | - Shaokai Wang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo N2L 3G1, Canada
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15
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Correa Marrero M, Jänes J, Baptista D, Beltrao P. Integrating Large-Scale Protein Structure Prediction into Human Genetics Research. Annu Rev Genomics Hum Genet 2024; 25:123-140. [PMID: 38621234 DOI: 10.1146/annurev-genom-120622-020615] [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: 04/17/2024]
Abstract
The last five years have seen impressive progress in deep learning models applied to protein research. Most notably, sequence-based structure predictions have seen transformative gains in the form of AlphaFold2 and related approaches. Millions of missense protein variants in the human population lack annotations, and these computational methods are a valuable means to prioritize variants for further analysis. Here, we review the recent progress in deep learning models applied to the prediction of protein structure and protein variants, with particular emphasis on their implications for human genetics and health. Improved prediction of protein structures facilitates annotations of the impact of variants on protein stability, protein-protein interaction interfaces, and small-molecule binding pockets. Moreover, it contributes to the study of host-pathogen interactions and the characterization of protein function. As genome sequencing in large cohorts becomes increasingly prevalent, we believe that better integration of state-of-the-art protein informatics technologies into human genetics research is of paramount importance.
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Affiliation(s)
- Miguel Correa Marrero
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland;
| | - Jürgen Jänes
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland;
| | | | - Pedro Beltrao
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland;
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16
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Cobley JN, Margaritelis NV, Chatzinikolaou PN, Nikolaidis MG, Davison GW. Ten "Cheat Codes" for Measuring Oxidative Stress in Humans. Antioxidants (Basel) 2024; 13:877. [PMID: 39061945 PMCID: PMC11273696 DOI: 10.3390/antiox13070877] [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: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Formidable and often seemingly insurmountable conceptual, technical, and methodological challenges hamper the measurement of oxidative stress in humans. For instance, fraught and flawed methods, such as the thiobarbituric acid reactive substances assay kits for lipid peroxidation, rate-limit progress. To advance translational redox research, we present ten comprehensive "cheat codes" for measuring oxidative stress in humans. The cheat codes include analytical approaches to assess reactive oxygen species, antioxidants, oxidative damage, and redox regulation. They provide essential conceptual, technical, and methodological information inclusive of curated "do" and "don't" guidelines. Given the biochemical complexity of oxidative stress, we present a research question-grounded decision tree guide for selecting the most appropriate cheat code(s) to implement in a prospective human experiment. Worked examples demonstrate the benefits of the decision tree-based cheat code selection tool. The ten cheat codes define an invaluable resource for measuring oxidative stress in humans.
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Affiliation(s)
- James N. Cobley
- The University of Dundee, Dundee DD1 4HN, UK
- Ulster University, Belfast BT15 1ED, Northern Ireland, UK;
| | - Nikos V. Margaritelis
- Aristotle University of Thessaloniki, 62122 Serres, Greece; (N.V.M.); (P.N.C.); (M.G.N.)
| | | | - Michalis G. Nikolaidis
- Aristotle University of Thessaloniki, 62122 Serres, Greece; (N.V.M.); (P.N.C.); (M.G.N.)
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17
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Huang CF, Hollas MA, Sanchez A, Bhattacharya M, Ho G, Sundaresan A, Caldwell MA, Zhao X, Benz R, Siddiqui A, Kelleher NL. Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.20.604425. [PMID: 39071411 PMCID: PMC11275834 DOI: 10.1101/2024.07.20.604425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The dynamic range challenge for detection of proteins and their proteoforms in human plasma has been well documented. Here, we use the nanoparticle protein corona approach to enrich low-abundant proteins selectively and reproducibly from human plasma and use top-down proteomics to quantify differential enrichment for the 2841 detected proteoforms from 114 proteins. Furthermore, nanoparticle enrichment allowed top-down detection of proteoforms between ∼1 µg/mL and ∼10 pg/mL in absolute abundance, providing up to 10 5 -fold increase in proteome depth over neat plasma in which only proteoforms from abundant proteins (>1 µg/mL) were detected. The ability to monitor medium and some low abundant proteoforms through reproducible enrichment significantly extends the applicability of proteoform research by adding depth beyond albumin, immunoglobins and apolipoproteins to uncover many involved in immunity and cell signaling. As proteoforms carry unique information content relative to peptides, this report opens the door to deeper proteoform sequencing in clinical proteomics of disease or aging cohorts.
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18
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Xu T, Wang Q, Wang Q, Sun L. Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4664-4682. [PMID: 38973469 PMCID: PMC11257149 DOI: 10.1039/d4ay00651h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
Proteoforms are all forms of protein molecules from the same gene because of variations at the DNA, RNA, and protein levels, e.g., alternative splicing and post-translational modifications (PTMs). Delineation of proteins in a proteoform-specific manner is crucial for understanding their biological functions. Mass spectrometry (MS)-intensive top-down proteomics (TDP) is promising for comprehensively characterizing intact proteoforms in complex biological systems. It has achieved substantial progress in technological development, including sample preparation, proteoform separations, MS instrumentation, and bioinformatics tools. In a single TDP study, thousands of proteoforms can be identified and quantified from a cell lysate. It has also been applied to various biomedical research to better our understanding of protein function in regulating cellular processes and to discover novel proteoform biomarkers of diseases for early diagnosis and therapeutic development. This review covers the most recent technological development and biomedical applications of MS-intensive TDP.
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Affiliation(s)
- Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
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19
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Roberts DS, Loo JA, Tsybin YO, Liu X, Wu S, Chamot-Rooke J, Agar JN, Paša-Tolić L, Smith LM, Ge Y. Top-down proteomics. NATURE REVIEWS. METHODS PRIMERS 2024; 4:38. [PMID: 39006170 PMCID: PMC11242913 DOI: 10.1038/s43586-024-00318-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 07/16/2024]
Abstract
Proteoforms, which arise from post-translational modifications, genetic polymorphisms and RNA splice variants, play a pivotal role as drivers in biology. Understanding proteoforms is essential to unravel the intricacies of biological systems and bridge the gap between genotypes and phenotypes. By analysing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and can decipher protein function, uncover disease mechanisms and advance precision medicine. This Primer explores TDP, including the underlying principles, recent advances and an outlook on the future. The experimental section discusses instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques and data collection. The results section looks at how to decipher raw data, visualize intact protein spectra and unravel data analysis. Additionally, proteoform identification, characterization and quantification are summarized, alongside approaches for statistical analysis. Various applications are described, including the human proteoform project and biomedical, biopharmaceutical and clinical sciences. These are complemented by discussions on measurement reproducibility, limitations and a forward-looking perspective that outlines areas where the field can advance, including potential future applications.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California - Los Angeles, Los Angeles, CA, USA
| | | | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, USA
| | | | - Jeffrey N Agar
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Ljiljana Paša-Tolić
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
- Department of Cell and Regenerative Biology, Human Proteomics Program, University of Wisconsin - Madison, Madison, WI, USA
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20
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Su P, Hollas MAR, Butun FA, Kanchustambham VL, Rubakhin S, Ramani N, Greer JB, Early BP, Fellers RT, Caldwell MA, Sweedler JV, Kafader JO, Kelleher NL. Single Cell Analysis of Proteoforms. J Proteome Res 2024; 23:1883-1893. [PMID: 38497708 PMCID: PMC11406863 DOI: 10.1021/acs.jproteome.4c00075] [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] [Indexed: 03/19/2024]
Abstract
We introduce single cell Proteoform imaging Mass Spectrometry (scPiMS), which realizes the benefit of direct solvent extraction and MS detection of intact proteins from single cells dropcast onto glass slides. Sampling and detection of whole proteoforms by individual ion mass spectrometry enable a scalable approach to single cell proteomics. This new scPiMS platform addresses the throughput bottleneck in single cell proteomics and boosts the cell processing rate by several fold while accessing protein composition with higher coverage.
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Affiliation(s)
- Pei Su
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael A R Hollas
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Fatma Ayaloglu Butun
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Vijaya Lakshmi Kanchustambham
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Stanislav Rubakhin
- Beckman Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Namrata Ramani
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Joseph B Greer
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Bryan P Early
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Ryan T Fellers
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael A Caldwell
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Jonathan V Sweedler
- Beckman Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jared O Kafader
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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21
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Zhai Z, Mavridou D, Damian M, Mutti FG, Schoenmakers PJ, Gargano AFG. Characterization of Complex Proteoform Mixtures by Online Nanoflow Ion-Exchange Chromatography-Native Mass Spectrometry. Anal Chem 2024; 96:8880-8885. [PMID: 38771719 PMCID: PMC11154664 DOI: 10.1021/acs.analchem.4c01760] [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: 04/03/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/23/2024]
Abstract
The characterization of proteins and complexes in biological systems is essential to establish their critical properties and to understand their unique functions in a plethora of bioprocesses. However, it is highly difficult to analyze low levels of intact proteins in their native states (especially those exceeding 30 kDa) with liquid chromatography (LC)-mass spectrometry (MS). Herein, we describe for the first time the use of nanoflow ion-exchange chromatography directly coupled with native MS to resolve mixtures of intact proteins. Reference proteins and protein complexes with molecular weights between 10 and 150 kDa and a model cell lysate were separated using a salt-mediated pH gradient method with volatile additives. The method allowed for low detection limits (0.22 pmol of monoclonal antibodies), while proteins presented nondenatured MS (low number of charges and limited charge state distributions), and the oligomeric state of the complexes analyzed was mostly kept. Excellent chromatographic separations including the resolution of different proteoforms of large proteins (>140 kDa) and a peak capacity of 82 in a 30 min gradient were obtained. The proposed setup and workflows show great potential for analyzing diverse proteoforms in native top-down proteomics, opening unprecedented opportunities for clinical studies and other sample-limited applications.
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Affiliation(s)
- Ziran Zhai
- Analytical
Chemistry Group and Biocatalysis Group, Van’t Hoff Institute
for Molecular Sciences (HIMS), University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Centre
for Analytical Sciences Amsterdam, Van’t Hoff Institute for
Molecular Sciences (HIMS), University of
Amsterdam, Science Park
904, 1098 XH Amsterdam, The Netherlands
| | - Despoina Mavridou
- Analytical
Chemistry Group and Biocatalysis Group, Van’t Hoff Institute
for Molecular Sciences (HIMS), University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Centre
for Analytical Sciences Amsterdam, Van’t Hoff Institute for
Molecular Sciences (HIMS), University of
Amsterdam, Science Park
904, 1098 XH Amsterdam, The Netherlands
| | - Matteo Damian
- Analytical
Chemistry Group and Biocatalysis Group, Van’t Hoff Institute
for Molecular Sciences (HIMS), University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Francesco G. Mutti
- Analytical
Chemistry Group and Biocatalysis Group, Van’t Hoff Institute
for Molecular Sciences (HIMS), University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Peter J. Schoenmakers
- Analytical
Chemistry Group and Biocatalysis Group, Van’t Hoff Institute
for Molecular Sciences (HIMS), University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Centre
for Analytical Sciences Amsterdam, Van’t Hoff Institute for
Molecular Sciences (HIMS), University of
Amsterdam, Science Park
904, 1098 XH Amsterdam, The Netherlands
| | - Andrea F. G. Gargano
- Analytical
Chemistry Group and Biocatalysis Group, Van’t Hoff Institute
for Molecular Sciences (HIMS), University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Centre
for Analytical Sciences Amsterdam, Van’t Hoff Institute for
Molecular Sciences (HIMS), University of
Amsterdam, Science Park
904, 1098 XH Amsterdam, The Netherlands
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22
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Ohayon S, Taib L, Verma NC, Iarossi M, Bhattacharya I, Marom B, Huttner D, Meller A. Full-Length Single Protein Molecules Tracking and Counting in Thin Silicon Channels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2314319. [PMID: 38461367 DOI: 10.1002/adma.202314319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/25/2024] [Indexed: 03/11/2024]
Abstract
Emerging single-molecule protein sensing techniques are ushering in a transformative era in biomedical research. Nevertheless, challenges persist in realizing ultra-fast full-length protein sensing, including loss of molecular integrity due to protein fragmentation, biases introduced by antibodies affinity, identification of proteoforms, and low throughputs. Here, a single-molecule method for parallel protein separation and tracking is introduced, yielding multi-dimensional molecular properties used for their identification. Proteins are tagged by chemo-selective dual amino-acid specific labels and are electrophoretically separated by their mass/charge in custom-designed thin silicon channel with subwavelength height. This approach allows analysis of thousands of individual proteins within a few minutes by tracking their motion during the migration. The power of the method is demonstrated by quantifying a cytokine panel for host-response discrimination between viral and bacterial infections. Moreover, it is shown that two clinically-relevant splice isoforms of Vascular endothelial growth factor (VEGF) can be accurately quantified from human serum samples. Being non-destructive and compatible with full-length intact proteins, this method opens up ways for antibody-free single-protein molecule quantification.
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Affiliation(s)
- Shilo Ohayon
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Liran Taib
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | | | - Marzia Iarossi
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Ivy Bhattacharya
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Barak Marom
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Diana Huttner
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Amit Meller
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
- Russell Berrie Nanotechnology Institute, Technion-IIT, Haifa, 3200003, Israel
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23
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Habeck T, Brown KA, Des Soye B, Lantz C, Zhou M, Alam N, Hossain MA, Jung W, Keener JE, Volny M, Wilson JW, Ying Y, Agar JN, Danis PO, Ge Y, Kelleher NL, Li H, Loo JA, Marty MT, Paša-Tolić L, Sandoval W, Lermyte F. Top-down mass spectrometry of native proteoforms and their complexes: a community study. Nat Methods 2024:10.1038/s41592-024-02279-6. [PMID: 38744918 DOI: 10.1038/s41592-024-02279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.
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Affiliation(s)
- Tanja Habeck
- Technische Universität Darmstadt, Darmstadt, Germany
| | - Kyle A Brown
- University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Mowei Zhou
- Pacific Northwest National Laboratory, Richland, WA, USA
- Zhejiang University, Zhejiang, China
| | | | | | | | | | | | - Jesse W Wilson
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yujia Ying
- Sun Yat-sen University, Guangzhou, China
| | - Jeffrey N Agar
- Northeastern University, Boston, MA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Paul O Danis
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Ying Ge
- University of Wisconsin-Madison, Madison, WI, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Neil L Kelleher
- Northwestern University, Evanston, IL, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Huilin Li
- Sun Yat-sen University, Guangzhou, China
| | - Joseph A Loo
- University of California, Los Angeles, CA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | | | - Ljiljana Paša-Tolić
- Pacific Northwest National Laboratory, Richland, WA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
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24
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Naryzhny S. Puzzle of Proteoform Variety-Where Is a Key? Proteomes 2024; 12:15. [PMID: 38804277 PMCID: PMC11130821 DOI: 10.3390/proteomes12020015] [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: 01/31/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different.
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Affiliation(s)
- Stanislav Naryzhny
- B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Leningrad Region, Gatchina 188300, Russia
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25
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Kurgan N, Kjærgaard Larsen J, Deshmukh AS. Harnessing the power of proteomics in precision diabetes medicine. Diabetologia 2024; 67:783-797. [PMID: 38345659 DOI: 10.1007/s00125-024-06097-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 03/21/2024]
Abstract
Precision diabetes medicine (PDM) aims to reduce errors in prevention programmes, diagnosis thresholds, prognosis prediction and treatment strategies. However, its advancement and implementation are difficult due to the heterogeneity of complex molecular processes and environmental exposures that influence an individual's disease trajectory. To address this challenge, it is imperative to develop robust screening methods for all areas of PDM. Innovative proteomic technologies, alongside genomics, have proven effective in precision cancer medicine and are showing promise in diabetes research for potential translation. This narrative review highlights how proteomics is well-positioned to help improve PDM. Specifically, a critical assessment of widely adopted affinity-based proteomic technologies in large-scale clinical studies and evidence of the benefits and feasibility of using MS-based plasma proteomics is presented. We also present a case for the use of proteomics to identify predictive protein panels for type 2 diabetes subtyping and the development of clinical prediction models for prevention, diagnosis, prognosis and treatment strategies. Lastly, we discuss the importance of plasma and tissue proteomics and its integration with genomics (proteogenomics) for identifying unique type 2 diabetes intra- and inter-subtype aetiology. We conclude with a call for action formed on advancing proteomics technologies, benchmarking their performance and standardisation across sites, with an emphasis on data sharing and the inclusion of diverse ancestries in large cohort studies. These efforts should foster collaboration with key stakeholders and align with ongoing academic programmes such as the Precision Medicine in Diabetes Initiative consortium.
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Affiliation(s)
- Nigel Kurgan
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Kjærgaard Larsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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26
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Yang J, Ostafe R, Bruening ML. In-Membrane Enrichment and Peptic Digestion to Facilitate Analysis of Monoclonal Antibody Glycosylation. Anal Chem 2024; 96:6347-6355. [PMID: 38607313 PMCID: PMC11283323 DOI: 10.1021/acs.analchem.4c00030] [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] [Indexed: 04/13/2024]
Abstract
The number of therapeutic monoclonal antibodies (mAbs) is growing rapidly due to their widespread use for treating various diseases and health conditions. Assessing the glycosylation profile of mAbs during production is essential to ensuring their safety and efficacy. This research aims to rapidly isolate and digest mAbs for liquid chromatography-tandem mass spectrometry (LC-MS/MS) identification of glycans and monitoring of glycosylation patterns, potentially during manufacturing. Immobilization of an Fc region-specific ligand, oFc20, in a porous membrane enables the enrichment of mAbs from cell culture supernatant and efficient elution with an acidic solution. Subsequent digestion of the mAb eluate occurred in a pepsin-modified membrane within 5 min. The procedure does not require alkylation and desalting, greatly shortening the sample preparation time. Subsequent LC-MS/MS analysis identified 11 major mAb N-glycan proteoforms and assessed the relative peak areas of the glycosylated peptides. This approach is suitable for the glycosylation profiling of various human IgG mAbs, including biosimilars and different IgG subclasses. The total time required for this workflow is less than 2 h, whereas the conventional enzymatic release and labeling of glycans can take much longer. Thus, the integrated membranes are suitable for facilitating the analysis of mAb glycosylation patterns.
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Affiliation(s)
- Junyan Yang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production Facility; Purdue Institute for Inflammation, Immunology and Infection Diseases, Purdue University, West Lafayette, IN 47907, United States
| | - Merlin L. Bruening
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
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27
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Makey DM, Gadkari VV, Kennedy RT, Ruotolo BT. Cyclic Ion Mobility-Mass Spectrometry and Tandem Collision Induced Unfolding for Quantification of Elusive Protein Biomarkers. Anal Chem 2024; 96:6021-6029. [PMID: 38557001 PMCID: PMC11081454 DOI: 10.1021/acs.analchem.4c00477] [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] [Indexed: 04/04/2024]
Abstract
Sensitive analytical techniques that are capable of detecting and quantifying disease-associated biomolecules are indispensable in our efforts to understand disease mechanisms and guide therapeutic intervention through early detection, accurate diagnosis, and effective monitoring of disease. Parkinson's Disease (PD), for example, is one of the most prominent neurodegenerative disorders in the world, but the diagnosis of PD has primarily been based on the observation of clinical symptoms. The protein α-synuclein (α-syn) has emerged as a promising biomarker candidate for PD, but a lack of analytical methods to measure complex disease-associated variants of α-syn has prevented its widespread use as a biomarker. Antibody-based methods such as immunoassays and mass spectrometry-based approaches have been used to measure a limited number of α-syn forms; however, these methods fail to differentiate variants of α-syn that display subtle differences in only the sequence and structure. In this work, we developed a cyclic ion mobility-mass spectrometry method that combines multiple stages of activation and timed ion selection to quantify α-syn variants using both mass- and structure-based measurements. This method can allow for the quantification of several α-syn variants present at physiological levels in biological fluid. Taken together, this approach can be used to galvanize future efforts aimed at understanding the underlying mechanisms of PD and serves as a starting point for the development of future protein-structure-based diagnostics and therapeutic interventions.
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Affiliation(s)
- Devin M. Makey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V. Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Robert T. Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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28
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D’Ippolito R, Rabara D, Blanco MA, Alberico E, Drew MR, Ramakrishnan N, Sontan D, Widmeyer SRT, Scheidemantle GM, Messing S, Turner D, Arkin M, Maciag AE, Stephen AG, Esposito D, McCormick F, Nissley DV, DeHart CJ. A Top-Down Proteomic Assay to Evaluate KRAS4B-Compound Engagement. Anal Chem 2024; 96:5223-5231. [PMID: 38498381 PMCID: PMC10993199 DOI: 10.1021/acs.analchem.3c05626] [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: 12/11/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024]
Abstract
Development of new targeted inhibitors for oncogenic KRAS mutants may benefit from insight into how a given mutation influences the accessibility of protein residues and how compounds interact with mutant or wild-type KRAS proteins. Targeted proteomic analysis, a key validation step in the KRAS inhibitor development process, typically involves both intact mass- and peptide-based methods to confirm compound localization or quantify binding. However, these methods may not always provide a clear picture of the compound binding affinity for KRAS, how specific the compound is to the target KRAS residue, and how experimental conditions may impact these factors. To address this, we have developed a novel top-down proteomic assay to evaluate in vitro KRAS4B-compound engagement while assessing relative quantitation in parallel. We present two applications to demonstrate the capabilities of our assay: maleimide-biotin labeling of a KRAS4BG12D cysteine mutant panel and treatment of three KRAS4B proteins (WT, G12C, and G13C) with small molecule compounds. Our results show the time- or concentration-dependence of KRAS4B-compound engagement in context of the intact protein molecule while directly mapping the compound binding site.
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Affiliation(s)
- Robert
A. D’Ippolito
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Dana Rabara
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Maria Abreu Blanco
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Emily Alberico
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Matthew R. Drew
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Nitya Ramakrishnan
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Dara Sontan
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Stephanie R. T. Widmeyer
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Grace M. Scheidemantle
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Simon Messing
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - David Turner
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Michelle Arkin
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, California 94143, United States
- Small
Molecule Discovery Center, University of
California, San Francisco, California 94143, United States
| | - Anna E. Maciag
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Andrew G. Stephen
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Dominic Esposito
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Frank McCormick
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Helen
Diller Family Comprehensive Cancer Center, University of California, San
Francisco, California 94158, United States
| | - Dwight V. Nissley
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Caroline J. DeHart
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
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29
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König S, Schork K, Eisenacher M. Observations from the Proteomics Bench. Proteomes 2024; 12:6. [PMID: 38390966 PMCID: PMC10885119 DOI: 10.3390/proteomes12010006] [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: 12/28/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
Many challenges in proteomics result from the high-throughput nature of the experiments. This paper first presents pre-analytical problems, which still occur, although the call for standardization in omics has been ongoing for many years. This article also discusses aspects that affect bioinformatic analysis based on three sets of reference data measured with different orbitrap instruments. Despite continuous advances in mass spectrometer technology as well as analysis software, data-set-wise quality control is still necessary, and decoy-based estimation, although challenged by modern instruments, should be utilized. We draw attention to the fact that numerous young researchers perceive proteomics as a mature, readily applicable technology. However, it is important to emphasize that the maximum potential of the technology can only be realized by an educated handling of its limitations.
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Affiliation(s)
- Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
| | - Karin Schork
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Ruhr-University Bochum, 44801 Bochum, Germany
- Core Unit for Bioinformatics (CUBiMed.RUB), Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Ruhr-University Bochum, 44801 Bochum, Germany
- Core Unit for Bioinformatics (CUBiMed.RUB), Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
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30
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Rogers HT, Melby JA, Ehlers LE, Fischer MS, Larson EJ, Gao Z, Rossler KJ, Wang D, Alpert AJ, Ge Y. Small-Scale Serial Size Exclusion Chromatography (s 3SEC) for High Sensitivity Top-Down Proteomics of Large Proteoforms. Anal Chem 2024:10.1021/acs.analchem.3c05733. [PMID: 38315630 PMCID: PMC11298573 DOI: 10.1021/acs.analchem.3c05733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Top-down-mass spectrometry (MS)-based proteomics has emerged as a premier technology to examine proteins at the proteoform level, enabling characterization of genetic mutations, alternative splicing, and post-translational modifications. However, significant challenges that remain in top-down proteomics include the analysis of large proteoforms and the sensitivity required to examine proteoforms from minimal amounts of sample. To address these challenges, we have developed a new method termed "small-scale serial Size Exclusion Chromatography" (s3SEC), which incorporates a small-scale protein extraction (1 mg of tissue) and serial SEC without postfractionation sample handling, coupled with online high sensitivity capillary reversed-phase liquid chromatography tandem MS (RPLC-MS/MS) for analysis of large proteoforms. The s3SEC-RPLC-MS/MS method significantly enhanced the sensitivity and reduced the proteome complexity across the fractions, enabling the detection of high MW proteoforms previously undetected in one-dimensional (1D)-RPLC analysis. Importantly, we observed a drastic improvement in the signal intensity of high MW proteoforms in early fractions when using the s3SEC-RPLC method. Moreover, we demonstrate that this s3SEC-RPLC-MS/MS method also allows the analysis of lower MW proteoforms in subsequent fractions without significant alteration in proteoform abundance and equivalent or improved fragmentation efficiency to that of the 1D-RPLC approach. Although this study focuses on the use of cardiac tissue, the s3SEC-RPLC-MS/MS method could be broadly applicable to other systems with limited sample inputs.
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Affiliation(s)
- Holden T. Rogers
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Lauren E. Ehlers
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Matthew S. Fischer
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Eli J. Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Zhan Gao
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Kalina J. Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | | | | | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
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31
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Green JJ, Grimm C, Fristo A, Byrum J, Kelleher NL. Parsing 20 Years of Public Data by AI Maps Trends in Proteomics and Forecasts Technology. J Proteome Res 2024; 23:523-531. [PMID: 38096378 PMCID: PMC10874502 DOI: 10.1021/acs.jproteome.3c00430] [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] [Indexed: 01/28/2024]
Abstract
The trends of the last 20 years in biotechnology were revealed using artificial intelligence and natural language processing (NLP) of publicly available data. Implementing this "science-of-science" approach, we capture convergent trends in the field of proteomics in both technology development and application across the phylogenetic tree of life. With major gaps in our knowledge about protein composition, structure, and location over time, we report trends in persistent, popular approaches and emerging technologies across 94 ideas from a corpus of 29 journals in PubMed over two decades. New metrics for clusters of these ideas reveal the progression and popularity of emerging approaches like single-cell, spatial, compositional, and chemical proteomics designed to better capture protein-level chemistry and biology. This analysis of the proteomics literature with advanced analytic tools quantifies the Rate of Rise for a next generation of technologies to better define, quantify, and visualize the multiple dimensions of the proteome that will transform our ability to measure and understand proteins in the coming decade.
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Affiliation(s)
- Josiah J. Green
- Consilience, Inc., 36 Muzzey Street, Lexington, MA 02421, USA
| | - Chase Grimm
- Consilience, Inc., 36 Muzzey Street, Lexington, MA 02421, USA
| | - Andre Fristo
- Consilience, Inc., 36 Muzzey Street, Lexington, MA 02421, USA
| | - Joseph Byrum
- Consilience, Inc., 36 Muzzey Street, Lexington, MA 02421, USA
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
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32
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Tholey A, Schlüter H. Top-down proteomics and proteoforms - special issue. Proteomics 2024; 24:e2200375. [PMID: 38351467 DOI: 10.1002/pmic.202200375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 02/16/2024]
Affiliation(s)
- Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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33
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Takemori A, Kaulich PT, Konno R, Kawashima Y, Hamazaki Y, Hoshino A, Tholey A, Takemori N. GeLC-FAIMS-MS workflow for in-depth middle-down proteomics. Proteomics 2024; 24:e2200431. [PMID: 37548120 DOI: 10.1002/pmic.202200431] [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: 04/14/2023] [Revised: 06/20/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Middle-down proteomics (MDP) is an analytical approach in which protein samples are digested with proteases such as Glu-C to generate large peptides (>3 kDa) that are analyzed by mass spectrometry (MS). This method is useful for characterizing high-molecular-weight proteins that are difficult to detect by top-down proteomics (TDP), in which intact proteins are analyzed by MS. In this study, we applied GeLC-FAIMS-MS, a multidimensional separation workflow that combines gel-based prefractionation with LC-FAIMS MS, for deep MDP. Middle-down peptides generated by optimized limited Glu-C digestion conditions were first size-fractionated by polyacrylamide gel electrophoresis, followed by C4 reversed-phase liquid chromatography separation and additional ion mobility fractionation, resulting in a significant increase in peptide length detectable by MS. In addition to global analysis, the GeLC-FAIMS-MS concept can also be applied to targeted MDP, where only proteins in the desired molecular weight range are gel-fractionated and their Glu-C digestion products are analyzed, as demonstrated by targeted analysis of integrins in exosomes. In-depth MDP achieved by global and targeted GeLC-FAIMS-MS supports the exploration of proteoform information not covered by conventional TDP by increasing the number of detectable protein groups or post-translational modifications (PTMs) and improving the sequence coverage.
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Affiliation(s)
- Ayako Takemori
- Advanced Research Support Center, Institute for Promotion of Science and Technology, Ehime University, Ehime, Japan
| | - Philipp T Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Yuto Hamazaki
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Ayuko Hoshino
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Nobuaki Takemori
- Advanced Research Support Center, Institute for Promotion of Science and Technology, Ehime University, Ehime, Japan
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34
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Berthias F, Bilgin N, Mecinović J, Jensen ON. Top-down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms. Proteomics 2024; 24:e2200471. [PMID: 38282202 DOI: 10.1002/pmic.202200471] [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: 07/09/2023] [Revised: 11/15/2023] [Accepted: 12/12/2023] [Indexed: 01/30/2024]
Abstract
Enzymatic catalysis is one of the fundamental processes that drives the dynamic landscape of post-translational modifications (PTMs), expanding the structural and functional diversity of proteins. Here, we assessed enzyme specificity using a top-down ion mobility spectrometry (IMS) and tandem mass spectrometry (MS/MS) workflow. We successfully applied trapped IMS (TIMS) to investigate site-specific N-ε-acetylation of lysine residues of full-length histone H4 catalyzed by histone lysine acetyltransferase KAT8. We demonstrate that KAT8 exhibits a preference for N-ε-acetylation of residue K16, while also adding acetyl groups on residues K5 and K8 as the first degree of acetylation. Achieving TIMS resolving power values of up to 300, we fully separated mono-acetylated regioisomers (H4K5ac, H4K8ac, and H4K16ac). Each of these separated regioisomers produce unique MS/MS fragment ions, enabling estimation of their individual mobility distributions and the exact localization of the N-ε-acetylation sites. This study highlights the potential of top-down TIMS-MS/MS for conducting enzymatic assays at the intact protein level and, more generally, for separation and identification of intact isomeric proteoforms and precise PTM localization.
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Affiliation(s)
- Francis Berthias
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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Lin Y, Du C, Ying H, Zhou Y, Kong F, Zhao H, Lan M. Multiply-mesoporous hydrophilic titanium dioxide nanohybrid for the highly-performed enrichment of N-glycopeptides from human serum. Anal Chim Acta 2024; 1287:342058. [PMID: 38182336 DOI: 10.1016/j.aca.2023.342058] [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: 08/30/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/07/2024]
Abstract
N-glycopeptide is considered as one of significant biomarkers which provide guidance for the diagnosis and drug design of diseases. However, the direct analysis of N-glycopeptides is nearly impracticable mainly owing to their extremely low abundance and grave signal suppression from other interfering substances in the bio-samples. In this research, a multiply-mesoporous hydrophilic TiO2 nanohybrid (mM-TiO2@Cys) was synthesized by immobilizing Cys on a TiO2 substrate with hierarchical mesopores to achieve the highly-performed enrichment of N-glycopeptides. With the advantages of superior hydrophilicity and multiply-mesoporous structure, the obtained material exhibited an excellent selectivity (IgG digests and BSA digests at the molar ratio of 1/500), a high sensitivity (1 fmol μL-1 for IgG digests) and a good size-exclusion ability (IgG digests, IgG and BSA at the molar ratio of 1/500/500) in the enrichment of N-glycopeptides from IgG digests. As a result, 281 N-glycopeptides corresponded with 109 glycoproteins were identified from 2 μL serum digests of the patients with nasopharyngeal carcinoma, and 181 N-glycopeptides corresponded with 78 glycoproteins were identified from 2 μL serum digests of the healthy volunteers, revealing the potential application value of mM-TiO2@Cys in glycoproteomics.
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Affiliation(s)
- Yunfan Lin
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chengrun Du
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Clinical Research Center for Radiation Oncology, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Shanghai, 200032, China
| | - Hongmei Ying
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Clinical Research Center for Radiation Oncology, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Shanghai, 200032, China.
| | - Yifan Zhou
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Fangfang Kong
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Clinical Research Center for Radiation Oncology, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Shanghai, 200032, China
| | - Hongli Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Santos LGC, Parreira VDSC, da Silva EMG, Santos MDM, Fernandes ADF, Neves-Ferreira AGDC, Carvalho PC, Freitas FCDP, Passetti F. SpliceProt 2.0: A Sequence Repository of Human, Mouse, and Rat Proteoforms. Int J Mol Sci 2024; 25:1183. [PMID: 38256255 PMCID: PMC10816255 DOI: 10.3390/ijms25021183] [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: 10/31/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
SpliceProt 2.0 is a public proteogenomics database that aims to list the sequence of known proteins and potential new proteoforms in human, mouse, and rat proteomes. This updated repository provides an even broader range of computationally translated proteins and serves, for example, to aid with proteomic validation of splice variants absent from the reference UniProtKB/SwissProt database. We demonstrate the value of SpliceProt 2.0 to predict orthologous proteins between humans and murines based on transcript reconstruction, sequence annotation and detection at the transcriptome and proteome levels. In this release, the annotation data used in the reconstruction of transcripts based on the methodology of ternary matrices were acquired from new databases such as Ensembl, UniProt, and APPRIS. Another innovation implemented in the pipeline is the exclusion of transcripts predicted to be susceptible to degradation through the NMD pathway. Taken together, our repository and its applications represent a valuable resource for the proteogenomics community.
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Affiliation(s)
- Letícia Graziela Costa Santos
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Vinícius da Silva Coutinho Parreira
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Esdras Matheus Gomes da Silva
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brazil 4036, Campus Maré, Rio de Janeiro 21040-361, RJ, Brazil
| | - Marlon Dias Mariano Santos
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Alexander da Franca Fernandes
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Ana Gisele da Costa Neves-Ferreira
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brazil 4036, Campus Maré, Rio de Janeiro 21040-361, RJ, Brazil
| | - Paulo Costa Carvalho
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Flávia Cristina de Paula Freitas
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luis, Km 235, São Carlos 13565-905, SP, Brazil
| | - Fabio Passetti
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
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Rossler KJ, de Lange WJ, Mann MW, Aballo TJ, Melby JA, Zhang J, Kim G, Bayne EF, Zhu Y, Farrell ET, Kamp TJ, Ralphe JC, Ge Y. Lactate- and immunomagnetic-purified hiPSC-derived cardiomyocytes generate comparable engineered cardiac tissue constructs. JCI Insight 2024; 9:e172168. [PMID: 37988170 PMCID: PMC10906451 DOI: 10.1172/jci.insight.172168] [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: 05/09/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
Three-dimensional engineered cardiac tissue (ECT) using purified human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) has emerged as an appealing model system for the study of human cardiac biology and disease. A recent study reported widely used metabolic (lactate) purification of monolayer hiPSC-CM cultures results in an ischemic cardiomyopathy-like phenotype compared with magnetic antibody-based cell sorting (MACS) purification, complicating the interpretation of studies using lactate-purified hiPSC-CMs. Herein, our objective was to determine if use of lactate relative to MACS-purified hiPSC-CMs affects the properties of resulting hiPSC-ECTs. Therefore, hiPSC-CMs were differentiated and purified using either lactate-based media or MACS. Global proteomics revealed that lactate-purified hiPSC-CMs displayed a differential phenotype over MACS hiPSC-CMs. hiPSC-CMs were then integrated into 3D hiPSC-ECTs and cultured for 4 weeks. Structurally, there was no significant difference in sarcomere length between lactate and MACS hiPSC-ECTs. Assessment of isometric twitch force and Ca2+ transient measurements revealed similar functional performance between purification methods. High-resolution mass spectrometry-based quantitative proteomics showed no significant difference in protein pathway expression or myofilament proteoforms. Taken together, this study demonstrates that lactate- and MACS-purified hiPSC-CMs generate ECTs with comparable structural, functional, and proteomic features, and it suggests that lactate purification does not result in an irreversible change in a hiPSC-CM phenotype.
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Affiliation(s)
- Kalina J. Rossler
- Molecular and Cellular Pharmacology Training Program
- Department of Cell and Regenerative Biology
| | | | | | - Timothy J. Aballo
- Molecular and Cellular Pharmacology Training Program
- Department of Cell and Regenerative Biology
| | | | | | | | | | - Yanlong Zhu
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Timothy J. Kamp
- Department of Cell and Regenerative Biology
- Department of Medicine
| | | | - Ying Ge
- Department of Cell and Regenerative Biology
- Department of Chemistry, and
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Di Tucci C, Muzii L. Chronic Pelvic Pain, Vulvar Pain Disorders, and Proteomics Profiles: New Discoveries, New Hopes. Biomedicines 2023; 12:1. [PMID: 38275362 PMCID: PMC10813718 DOI: 10.3390/biomedicines12010001] [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: 11/08/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Chronic pelvic pain (CPP) is generally defined as non-cyclic pain perceived in the pelvic area that has persisted from three to six months or longer and is unrelated to pregnancy. The etiology of CPP is complex, multifactorial, with heterogeneous presentation, and includes several diseases such as endometriosis, adenomyosis, and interstitial cystitis/bladder pain syndrome. It may also be associated with sexual dysfunction, musculoskeletal disorders, and comorbid psychiatric symptoms. Vulvar pain disorders (VPDs) are typically categorized separately from chronic pelvic pain; among all VPDs, vulvodynia is a chronic vulvar pain of unknown etiology, lasting at least 3 months and that might be associated with other potentially linked factors. Proteomics represents a useful approach to study the proteome profiles of clinical samples. In this review, we have considered a selection of articles that have analyzed the protein abundance and novel protein species from various biological samples, including eutopic/ectopic endometrium, urine, serum, follicular, peritoneal fluid, and cervical mucus, potentially involved in the pathogenesis and progression of CPP and VPDs. These findings could represent valuable targets for paving the way for the differential diagnosis and therapeutic management of CPP and VDPs, thereby optimizing both the prevention and treatment of these conditions.
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Affiliation(s)
- Chiara Di Tucci
- Department of Obstetrics and Gynecology, “Sapienza” University, 00185 Rome, Italy;
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Chapman EA, Roberts DS, Tiambeng TN, Andrews J, Wang MD, Reasoner EA, Melby JA, Li BH, Kim D, Alpert AJ, Jin S, Ge Y. Structure and dynamics of endogenous cardiac troponin complex in human heart tissue captured by native nanoproteomics. Nat Commun 2023; 14:8400. [PMID: 38110393 PMCID: PMC10728164 DOI: 10.1038/s41467-023-43321-z] [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: 07/04/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023] Open
Abstract
Protein complexes are highly dynamic entities that display substantial diversity in their assembly, post-translational modifications, and non-covalent interactions, allowing them to play critical roles in various biological processes. The heterogeneity, dynamic nature, and low abundance of protein complexes in their native states present challenges to study using conventional structural biology techniques. Here we develop a native nanoproteomics strategy for the enrichment and subsequent native top-down mass spectrometry (nTDMS) analysis of endogenous cardiac troponin (cTn) complex directly from human heart tissue. The cTn complex is enriched and purified using peptide-functionalized superparamagnetic nanoparticles under non-denaturing conditions to enable the isotopic resolution of cTn complex, revealing their complex structure and assembly. Moreover, nTDMS elucidates the stoichiometry and composition of the cTn complex, localizes Ca2+ binding domains, defines cTn-Ca2+ binding dynamics, and provides high-resolution mapping of the proteoform landscape. This native nanoproteomics strategy opens a paradigm for structural characterization of endogenous native protein complexes.
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Affiliation(s)
- Emily A Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Timothy N Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jãán Andrews
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Man-Di Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily A Reasoner
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brad H Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Donguk Kim
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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40
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Huang CF, Su P, Fisher TD, Levitsky J, Kelleher NL, Forte E. Mass spectrometry-based proteomics for advancing solid organ transplantation research. FRONTIERS IN TRANSPLANTATION 2023; 2:1286881. [PMID: 38993855 PMCID: PMC11235370 DOI: 10.3389/frtra.2023.1286881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/13/2023] [Indexed: 07/13/2024]
Abstract
Scarcity of high-quality organs, suboptimal organ quality assessment, unsatisfactory pre-implantation procedures, and poor long-term organ and patient survival are the main challenges currently faced by the solid organ transplant (SOT) field. New biomarkers for assessing graft quality pre-implantation, detecting, and predicting graft injury, rejection, dysfunction, and survival are critical to provide clinicians with invaluable prediction tools and guidance for personalized patients' treatment. Additionally, new therapeutic targets are also needed to reduce injury and rejection and improve transplant outcomes. Proteins, which underlie phenotypes, are ideal candidate biomarkers of health and disease statuses and therapeutic targets. A protein can exist in different molecular forms, called proteoforms. As the function of a protein depends on its exact composition, proteoforms can offer a more accurate basis for connection to complex phenotypes than protein from which they derive. Mass spectrometry-based proteomics has been largely used in SOT research for identification of candidate biomarkers and therapeutic intervention targets by so-called "bottom-up" proteomics (BUP). However, such BUP approaches analyze small peptides in lieu of intact proteins and provide incomplete information on the exact molecular composition of the proteins of interest. In contrast, "Top-down" proteomics (TDP), which analyze intact proteins retaining proteoform-level information, have been only recently adopted in transplantation studies and already led to the identification of promising proteoforms as biomarkers for organ rejection and dysfunction. We anticipate that the use of top-down strategies in combination with new technological advancements in single-cell and spatial proteomics could drive future breakthroughs in biomarker and therapeutic target discovery in SOT.
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Affiliation(s)
- Che-Fan Huang
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Pei Su
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Troy D. Fisher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Josh Levitsky
- Division of Gastroenterology and Hepatology, Comprehensive Transplant Center Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
| | - Eleonora Forte
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
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41
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Cobley JN. 50 shades of oxidative stress: A state-specific cysteine redox pattern hypothesis. Redox Biol 2023; 67:102936. [PMID: 37875063 PMCID: PMC10618833 DOI: 10.1016/j.redox.2023.102936] [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: 09/25/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
Oxidative stress is biochemically complex. Like primary colours, specific reactive oxygen species (ROS) and antioxidant inputs can be mixed to create unique "shades" of oxidative stress. Even a minimal redox module comprised of just 12 (ROS & antioxidant) inputs and 3 outputs (oxidative damage, cysteine-dependent redox-regulation, or both) yields over half a million "shades" of oxidative stress. The present paper proposes the novel hypothesis that: state-specific shades of oxidative stress, such as a discrete disease, are associated with distinct tell-tale cysteine oxidation patterns. The patterns are encoded by many parameters, from the identity of the oxidised proteins, the cysteine oxidation type, and magnitude. The hypothesis is conceptually grounded in distinct ROS and antioxidant inputs coalescing to produce unique cysteine oxidation outputs. And considers the potential biological significance of the holistic cysteine oxidation outputs. The literature supports the existence of state-specific cysteine oxidation patterns. Measuring and manipulating these patterns offer promising avenues for advancing oxidative stress research. The pattern inspired hypothesis provides a framework for understanding the complex biochemical nature of state-specific oxidative stress.
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Affiliation(s)
- James N Cobley
- Cysteine redox technology Group, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK.
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Pienkowski T, Kowalczyk T, Cysewski D, Kretowski A, Ciborowski M. Glioma and post-translational modifications: A complex relationship. Biochim Biophys Acta Rev Cancer 2023; 1878:189009. [PMID: 37913943 DOI: 10.1016/j.bbcan.2023.189009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023]
Abstract
Post-translational modifications (PTMs) are common covalent processes in biochemical pathways that alter protein function and activity. These modifications occur through proteolytic cleavage or attachment of modifying groups, such as phosphoryl, methyl, glycosyl, or acetyl groups, with one or more amino acid residues of a single protein. Some PTMs also present crosstalk abilities that affect both protein functionality and structure, creating new proteoforms. Any alteration in organism homeostasis may be a cancer hallmark. Cataloging PTMs and consequently, emerging proteoforms, present new therapeutic targets, approaches, and opportunities to discover additional discriminatory biomarkers in disease diagnostics. In this review, we focus on experimentally confirmed PTMs and their potential crosstalk in glioma research to introduce new opportunities for this tumor type, which emerge within the PTMomics area.
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Affiliation(s)
- Tomasz Pienkowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Tomasz Kowalczyk
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland; Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland
| | - Dominik Cysewski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland; Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland.
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Lai YH, Wang YS. Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions. MASS SPECTROMETRY REVIEWS 2023; 42:2426-2445. [PMID: 35686331 DOI: 10.1002/mas.21790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/27/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.
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Affiliation(s)
- Yin-Hung Lai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National United University, Miaoli, Taiwan, R.O.C
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, R.O.C
| | - Yi-Sheng Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
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Bertile F, Matallana-Surget S, Tholey A, Cristobal S, Armengaud J. Diversifying the concept of model organisms in the age of -omics. Commun Biol 2023; 6:1062. [PMID: 37857885 PMCID: PMC10587087 DOI: 10.1038/s42003-023-05458-x] [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: 06/21/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023] Open
Abstract
In today's post-genomic era, it is crucial to rethink the concept of model organisms. While a few historically well-established organisms, e.g. laboratory rodents, have enabled significant scientific breakthroughs, there is now a pressing need for broader inclusion. Indeed, new organisms and models, from complex microbial communities to holobionts, are essential to fully grasp the complexity of biological principles across the breadth of biodiversity. By fostering collaboration between biology, advanced molecular science and omics communities, we can collectively adopt new models, unraveling their molecular functioning, and uncovering fundamental mechanisms. This concerted effort will undoubtedly enhance human health, environmental quality, and biodiversity conservation.
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Affiliation(s)
- Fabrice Bertile
- Université de Strasbourg, CNRS, IPHC UMR 7178, 23 rue du Loess, 67037, Strasbourg Cedex 2, France.
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping, 581 85, Sweden
- Ikerbasque, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, Leioa, 48940, Spain
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
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Chen YC, Liao CC, Shui HA, Huang PH, Shih LJ. A Proteomics-Based Identification of the Biological Networks Mediating the Impact of Epigallocatechin-3-Gallate on Trophoblast Cell Migration and Invasion, with Potential Implications for Maternal and Fetal Health. Proteomes 2023; 11:31. [PMID: 37873873 PMCID: PMC10594419 DOI: 10.3390/proteomes11040031] [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: 07/13/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023] Open
Abstract
Trophoblast migration and invasion play crucial roles in placental development. However, the effects of (-)-epigallocatechin-3-gallate (EGCG) on trophoblast cell functions remain largely unexplored. In this study, we investigated the impact of EGCG on the survival of trophoblast cells and employed a proteomics analysis to evaluate its influence on trophoblast cell migration and invasion. Be-Wo trophoblast cells were treated with EGCG, and a zone closure assay was conducted to assess the cell migration and invasion. Subsequently, a proteomics analysis was performed on the treated and control groups, followed by a bioinformatics analysis to evaluate the affected biological pathways and protein networks. A quantitative real-time PCR and Western blot analysis were carried out to validate the proteomics findings. Our results showed that EGCG significantly suppressed the trophoblast migration and invasion at a concentration not affecting cell survival. The proteomics analysis revealed notable differences in the protein expression between the EGCG-treated and control groups. Specifically, EGCG downregulated the signaling pathways related to EIF2, mTOR, and estrogen response, as well as the processes associated with the cytoskeleton, extracellular matrix, and protein translation. Conversely, EGCG upregulated the pathways linked to lipid degradation and oxidative metabolism. The quantitative PCR showed that EGCG modulated protein expression by regulating gene transcription, and the Western blot analysis confirmed its impact on cytoskeleton and extracellular matrix reorganization. These findings suggest EGCG may inhibit trophoblast migration and invasion through multiple signaling pathways, highlighting the potential risks associated with consuming EGCG-containing products during pregnancy. Future research should investigate the impact of EGCG intake on maternal and fetal proteoforms.
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Affiliation(s)
- Yueh-Chung Chen
- Department of Medicine, School of Medicine, National Defense Medical Center, Taipei 114201, Taiwan;
- Division of Cardiology, Department of Internal Medicine, Taipei City Hospital, Renai Branch, Taipei 106243, Taiwan
- Department of Health Promotion and Gerontological Care, Taipei University of Marine Technology, Taipei 111078, Taiwan
- Department of Special Education, University of Taipei, Taipei 100234, Taiwan
| | - Chen-Chung Liao
- Mass Spectrometry Facility, Instrumentation Resource Center, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (C.-C.L.)
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Hao-Ai Shui
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114201, Taiwan
| | - Pei-Hsuan Huang
- Mass Spectrometry Facility, Instrumentation Resource Center, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (C.-C.L.)
| | - Li-Jane Shih
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114201, Taiwan
- Department of Medical Laboratory, Taoyuan Armed Forces General Hospital, Longtan, Taoyuan 325208, Taiwan
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46
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Liu FC, Ridgeway ME, Wootton CA, Theisen A, Panczyk EM, Meier F, Park MA, Bleiholder C. Top-Down Protein Analysis by Tandem-Trapped Ion Mobility Spectrometry/Mass Spectrometry (Tandem-TIMS/MS) Coupled with Ultraviolet Photodissociation (UVPD) and Parallel Accumulation/Serial Fragmentation (PASEF) MS/MS Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2232-2246. [PMID: 37638640 PMCID: PMC11162218 DOI: 10.1021/jasms.3c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
"Top-down" proteomics analyzes intact proteins and identifies proteoforms by their intact mass as well as the observed fragmentation pattern in tandem mass spectrometry (MS/MS) experiments. Recently, hybrid ion mobility spectrometry-mass spectrometry (IM/MS) methods have gained traction for top-down experiments, either by allowing top-down analysis of individual isomers or alternatively by improving signal/noise and dynamic range for fragment ion assignment. We recently described the construction of a tandem-trapped ion mobility spectrometer/mass spectrometer (tandem-TIMS/MS) coupled with an ultraviolet (UV) laser and demonstrated a proof-of-principle for top-down analysis by UV photodissociation (UVPD) at 2-3 mbar. The present work builds on this with an exploration of a top-down method that couples tandem-TIMS/MS with UVPD and parallel-accumulation serial fragmentation (PASEF) MS/MS analysis. We first survey types and structures of UVPD-specific fragment ions generated in the 2-3 mbar pressure regime of our instrument. Notably, we observe UVPD-induced fragment ions with multiple conformations that differ from those produced in the absence of UV irradiation. Subsequently, we discuss how MS/MS spectra of top-down fragment ions lend themselves ideally for probability-based scoring methods developed in the bottom-up proteomics field and how the ability to record automated PASEF-MS/MS spectra resolves ambiguities in the assignment of top-down fragment ions. Finally, we describe the coupling of tandem-TIMS/MS workflows with UVPD and PASEF-MS/MS analysis for native top-down protein analysis.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32304, USA
| | | | | | | | | | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747 Jena, Germany
| | | | - Christian Bleiholder
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32304, USA
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47
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Dey AK, Banarjee R, Boroumand M, Rutherford DV, Strassheim Q, Nyunt T, Olinger B, Basisty N. Translating Senotherapeutic Interventions into the Clinic with Emerging Proteomic Technologies. BIOLOGY 2023; 12:1301. [PMID: 37887011 PMCID: PMC10604147 DOI: 10.3390/biology12101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Cellular senescence is a state of irreversible growth arrest with profound phenotypic changes, including the senescence-associated secretory phenotype (SASP). Senescent cell accumulation contributes to aging and many pathologies including chronic inflammation, type 2 diabetes, cancer, and neurodegeneration. Targeted removal of senescent cells in preclinical models promotes health and longevity, suggesting that the selective elimination of senescent cells is a promising therapeutic approach for mitigating a myriad of age-related pathologies in humans. However, moving senescence-targeting drugs (senotherapeutics) into the clinic will require therapeutic targets and biomarkers, fueled by an improved understanding of the complex and dynamic biology of senescent cell populations and their molecular profiles, as well as the mechanisms underlying the emergence and maintenance of senescence cells and the SASP. Advances in mass spectrometry-based proteomic technologies and workflows have the potential to address these needs. Here, we review the state of translational senescence research and how proteomic approaches have added to our knowledge of senescence biology to date. Further, we lay out a roadmap from fundamental biological discovery to the clinical translation of senotherapeutic approaches through the development and application of emerging proteomic technologies, including targeted and untargeted proteomic approaches, bottom-up and top-down methods, stability proteomics, and surfaceomics. These technologies are integral for probing the cellular composition and dynamics of senescent cells and, ultimately, the development of senotype-specific biomarkers and senotherapeutics (senolytics and senomorphics). This review aims to highlight emerging areas and applications of proteomics that will aid in exploring new senescent cell biology and the future translation of senotherapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Nathan Basisty
- Translational Geroproteomics Unit, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (A.K.D.); (R.B.); (M.B.); (D.V.R.); (Q.S.); (T.N.); (B.O.)
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48
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Astarita G, Kelly RS, Lasky-Su J. Metabolomics and lipidomics strategies in modern drug discovery and development. Drug Discov Today 2023; 28:103751. [PMID: 37640150 PMCID: PMC10543515 DOI: 10.1016/j.drudis.2023.103751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Metabolomics and lipidomics have an increasingly pivotal role in drug discovery and development. In the context of drug discovery, monitoring changes in the levels or composition of metabolites and lipids relative to genetic variations yields functional insights, bolstering human genetics and (meta)genomic methodologies. This approach also sheds light on potential novel targets for therapeutic intervention. In the context of drug development, metabolite and lipid biomarkers contribute to enhanced success rates, promising a transformative impact on precision medicine. In this review, we deviate from analytical chemist-focused perspectives, offering an overview tailored to drug discovery. We provide introductory insight into state-of-the-art mass spectrometry (MS)-based metabolomics and lipidomics techniques utilized in drug discovery and development, drawing from the collective expertise of our research teams. We comprehensively outline the application of metabolomics and lipidomics in advancing drug discovery and development, spanning fundamental research, target identification, mechanisms of action, and the exploration of biomarkers.
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Affiliation(s)
- Giuseppe Astarita
- Georgetown University, Washington, DC, USA; Arkuda Therapeutics, Watertown, MA, USA.
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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49
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Zhang Y, Minami R, Tatsuno R, Gao W, Ueno M, Yamada A, Yoshida A, Sedanza MG, Arima K, Takatani T, Yamaguchi K, Oshima Y, Arakawa O. Wheat germ agglutinin affinity chromatography enrichment and glyco-proteomic characterization of tetrodotoxin-binding proteins from the plasma of cultured tiger pufferfish (Takifugu rubripes). Biosci Biotechnol Biochem 2023; 87:1155-1168. [PMID: 37458754 DOI: 10.1093/bbb/zbad095] [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: 05/03/2023] [Accepted: 07/07/2023] [Indexed: 09/24/2023]
Abstract
Efficient enrichment of tetrodotoxin (TTX)-binding proteins from the plasma of cultured tiger pufferfish (Takifugu rubripes) was achieved by ammonium sulfate fractionation and wheat germ agglutinin (WGA) affinity chromatography. The enrichment efficiency was validated by ultrafiltration-LC/MS-based TTX-binding assay and proteomics. Major proteins in the WGA-bound fraction were identified as isoform X1 (125 kDa) and X2 variants (88 and 79 kDa) derived from pufferfish saxitoxin and tetrodotoxin-binding protein (PSTBP) 1-like gene (LOC101075943). The 125-kDa X1 protein was found to be a novel member of the lipocalin family, having three tandemly repeated domains. X2 variants, X2α and X2β, were estimated to have two domains, and X2β is structurally related to Takifugu pardalis PSTBP2 in their domain type and arrangement. Among 11 potential N-glycosylation sites in the X2 precursor, 5 N-glycosylated Asn residues (N55, N89, N244, N308, and N449) were empirically determined. Structural relationships among PSTBP homologs and complexity of their proteoforms are discussed.
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Affiliation(s)
- Yafei Zhang
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
| | - Ryoma Minami
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Ryohei Tatsuno
- National Fisheries University, Japan Fisheries Research and Education Agency, Nagatahonmachi, Shimonoseki, Yamaguchi, Japan
| | - Wei Gao
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
- Dalian Blue Peptide Technology Research & Development Co., Ltd, Dalian, China
| | - Mikinori Ueno
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
| | - Akinori Yamada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
| | - Asami Yoshida
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
| | - Mary Grace Sedanza
- Institute of Aquaculture, College of Fisheries and Ocean Sciences, University of the Philippines Visayas, Miagao, Iloilo, Philippines
| | - Kazunari Arima
- Department of Chemistry, Graduate School of Science and Engineering, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Tomohiro Takatani
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
| | - Kenichi Yamaguchi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
| | - Yuji Oshima
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka, Japan
| | - Osamu Arakawa
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
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50
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Pinto AFM, Diedrich JK, Moresco JJ, Yates JR. Differential Precipitation of Proteins: A Simple Protein Fractionation Strategy to Gain Biological Insights with Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2025-2033. [PMID: 37527410 DOI: 10.1021/jasms.3c00182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Differential precipitation of proteins (DiffPOP) is a simple technique for fractionating complex protein mixtures. Using stepwise addition of acidified methanol, ten distinct subsets of proteins can be selectively precipitated by centrifugation and identified by mass spectrometry-based proteomics. We have previously shown that the ability of a protein to resist precipitation can be altered by drug binding, which enabled us to identify a novel drug-target interaction. Here, we show that the addition of DiffPOP to a standard LC-MS proteomics workflow results in a three-dimensional separation of peptides that increases protein coverage and peptide identifications. Importantly, DiffPOP reveals solubility differences between proteoforms, potentially providing valuable insights that are typically lost in bottom-up proteomics.
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Affiliation(s)
- Antonio F M Pinto
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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