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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. [PMID: 38973469 DOI: 10.1039/d4ay00651h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [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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2
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Faizi M, Fellers RT, Lu D, Drown BS, Jambhekar A, Lahav G, Kelleher NL, Gunawardena J. MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data. Bioinformatics 2024; 40:btae335. [PMID: 38796681 PMCID: PMC11157153 DOI: 10.1093/bioinformatics/btae335] [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: 06/16/2023] [Revised: 02/28/2024] [Accepted: 05/24/2024] [Indexed: 05/28/2024] Open
Abstract
MOTIVATION Post-translational modifications (PTMs) on proteins regulate protein structures and functions. A single protein molecule can possess multiple modification sites that can accommodate various PTM types, leading to a variety of different patterns, or combinations of PTMs, on that protein. Different PTM patterns can give rise to distinct biological functions. To facilitate the study of multiple PTMs on the same protein molecule, top-down mass spectrometry (MS) has proven to be a useful tool to measure the mass of intact proteins, thereby enabling even PTMs at distant sites to be assigned to the same protein molecule and allowing determination of how many PTMs are attached to a single protein. RESULTS We developed a Python module called MSModDetector that studies PTM patterns from individual ion mass spectrometry (I2MS) data. I2MS is an intact protein mass spectrometry approach that generates true mass spectra without the need to infer charge states. The algorithm first detects and quantifies mass shifts for a protein of interest and subsequently infers potential PTM patterns using linear programming. The algorithm is evaluated on simulated I2MS data and experimental I2MS data for the tumor suppressor protein p53. We show that MSModDetector is a useful tool for comparing a protein's PTM pattern landscape across different conditions. An improved analysis of PTM patterns will enable a deeper understanding of PTM-regulated cellular processes. AVAILABILITY AND IMPLEMENTATION The source code is available at https://github.com/marjanfaizi/MSModDetector.
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Affiliation(s)
- Marjan Faizi
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL 60208, United States
| | - Dan Lu
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
| | - Bryon S Drown
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL 60208, United States
| | - Ashwini Jambhekar
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
| | - Galit Lahav
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL 60208, United States
| | - Jeremy Gunawardena
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
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3
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Dowling P, Gargan S, Zweyer M, Henry M, Meleady P, Swandulla D, Ohlendieck K. Proteomic reference map for sarcopenia research: mass spectrometric identification of key muscle proteins of organelles, cellular signaling, bioenergetic metabolism and molecular chaperoning. Eur J Transl Myol 2024; 34. [PMID: 38787292 DOI: 10.4081/ejtm.2024.12565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
During the natural aging process, frailty is often associated with abnormal muscular performance. Although inter-individual differences exit, in most elderly the tissue mass and physiological functionality of voluntary muscles drastically decreases. In order to study age-related contractile decline, animal model research is of central importance in the field of biogerontology. Here we have analyzed wild type mouse muscle to establish a proteomic map of crude tissue extracts. Proteomics is an advanced and large-scale biochemical method that attempts to identify all accessible proteins in a given biological sample. It is a technology-driven approach that uses mass spectrometry for the characterization of individual protein species. Total protein extracts were used in this study in order to minimize the potential introduction of artefacts due to excess subcellular fractionation procedures. In this report, the proteomic survey of aged muscles has focused on organellar marker proteins, as well as proteins that are involved in cellular signaling, the regulation of ion homeostasis, bioenergetic metabolism and molecular chaperoning. Hence, this study has establish a proteomic reference map of a highly suitable model system for future aging research.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases, Bonn.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
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4
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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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5
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Sadeghi S, Chen W, Wang Q, Wang Q, Fang F, Liu X, Sun L. Pilot Evaluation of the Long-Term Reproducibility of Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Top-Down Proteomics of a Complex Proteome Sample. J Proteome Res 2024; 23:1399-1407. [PMID: 38417052 PMCID: PMC11002928 DOI: 10.1021/acs.jproteome.3c00872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/01/2024]
Abstract
Mass spectrometry (MS)-based top-down proteomics (TDP) has revolutionized biological research by measuring intact proteoforms in cells, tissues, and biofluids. Capillary zone electrophoresis-tandem MS (CZE-MS/MS) is a valuable technique for TDP, offering a high peak capacity and sensitivity for proteoform separation and detection. However, the long-term reproducibility of CZE-MS/MS in TDP remains unstudied, which is a crucial aspect for large-scale studies. This work investigated the long-term qualitative and quantitative reproducibility of CZE-MS/MS for TDP for the first time, focusing on a yeast cell lysate. Over 1000 proteoforms were identified per run across 62 runs using one linear polyacrylamide (LPA)-coated separation capillary, highlighting the robustness of the CZE-MS/MS technique. However, substantial decreases in proteoform intensity and identification were observed after some initial runs due to proteoform adsorption onto the capillary inner wall. To address this issue, we developed an efficient capillary cleanup procedure using diluted ammonium hydroxide, achieving high qualitative and quantitative reproducibility for the yeast sample across at least 23 runs. The data underscore the capability of CZE-MS/MS for large-scale quantitative TDP of complex samples, signaling its readiness for deployment in broad biological applications. The MS RAW files were deposited in ProteomeXchange Consortium with the data set identifier of PXD046651.
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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
| | - Wenrong Chen
- Department
of BioHealth Informatics, Indiana University-Purdue
University Indianapolis, 535 W Michigan Street, Indianapolis, Indiana 46202, United States
| | - Qianyi Wang
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianjie Wang
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Fei Fang
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Xiaowen Liu
- Deming
Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, Louisiana 70112, United States
| | - Liangliang Sun
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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6
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Zhan Z, Wang L. Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra. Bioinformatics 2024; 40:btae149. [PMID: 38498847 PMCID: PMC11212493 DOI: 10.1093/bioinformatics/btae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/05/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024] Open
Abstract
MOTIVATION Proteoform identification is an important problem in proteomics. The main task is to find a modified protein that best fits the input spectrum. To overcome the combinatorial explosion of possible proteoforms, the proteoform mass graph and spectrum mass graph are used to represent the protein database and the spectrum, respectively. The problem becomes finding an optimal alignment between the proteoform mass graph and the spectrum mass graph. Peak error correction is an important issue for computing an optimal alignment between the two input mass graphs. RESULTS We propose a faster algorithm for the error correction alignment of spectrum mass graph and proteoform mass graph problem and produce a program package TopMGFast. The newly designed algorithms require less space and running time so that we are able to compute global optimal alignments for the two input mass graphs in a reasonable time. For the local alignment version, experiments show that the running time of the new algorithm is reduced by 2.5 times. For the global alignment version, experiments show that the maximum mass errors between any pair of matched nodes in the alignments obtained by our method are within a small range as designed, while the alignments produced by the state-of-the-art method, TopMG, have very large maximum mass errors for many cases. The obtained alignment sizes are roughly the same for both TopMG and TopMGFast. Of course, TopMGFast needs more running time than TopMG. Therefore, our new algorithm can obtain more reliable global alignments within a reasonable time. This is the first time that global optimal error correction alignments can be obtained using real datasets. AVAILABILITY AND IMPLEMENTATION The source code of the algorithm is available at https://github.com/Zeirdo/TopMGFast.
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Affiliation(s)
- Zhaohui Zhan
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Lusheng Wang
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
- City University of Hong Kong Shenzhen Research Institution, ShenZhen, 518057, China
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Mokry RL, Monti CE, Rosas-Rogers S, Schumacher ML, Dash RK, Terhune SS. Replication efficiencies of human cytomegalovirus-infected epithelial cells are dependent on source of virus production. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585739. [PMID: 38562837 PMCID: PMC10983881 DOI: 10.1101/2024.03.19.585739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Human cytomegalovirus (HCMV) is a prevalent betaherpesvirus, and infection can lead to a range of symptomatology from mononucleosis to sepsis in immunocompromised individuals. HCMV is also the leading viral cause of congenital birth defects. Lytic replication is supported by many cell types with different kinetics and efficiencies leading to a plethora of pathologies. The goal of these studies was to elucidate HCMV replication efficiencies for viruses produced on different cell types upon infection of epithelial cells by combining experimental approaches with data-driven computational modeling. HCMV was generated from a common genetic background of TB40-BAC4, propagated on fibroblasts (TB40Fb) or epithelial cells (TB40Epi), and used to infect epithelial cells. We quantified cell-associated viral genomes (vDNA), protein levels (pUL44, pp28), and cell-free titers over time for each virus at different multiplicities of infection. We combined experimental quantification with data-driven simulations and determined that parameters describing vDNA synthesis were similar between sources. We found that pUL44 accumulation was higher in TB40Fb than TB40Epi. In contrast, pp28 accumulation was higher in TB40Epi which coincided with a significant increase in titer for TB40Epi over TB40Fb. These differences were most evident during live-cell imaging, which revealed syncytia-like formation during infection by TB40Epi. Simulations of the late lytic replication cycle yielded a larger synthesis constant for pp28 in TB40Epi along with increase in virus output despite similar rates of genome synthesis. By combining experimental and computational modeling approaches, our studies demonstrate that the cellular source of propagated virus impacts viral replication efficiency in target cell types.
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Affiliation(s)
- Rebekah L. Mokry
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Christopher E. Monti
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Suzette Rosas-Rogers
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Megan L. Schumacher
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Ranjan K. Dash
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI-53226
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Scott S. Terhune
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI-53226
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8
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Popova L, Carr RA, Carabetta VJ. Recent Contributions of Proteomics to Our Understanding of Reversible N ε-Lysine Acylation in Bacteria. J Proteome Res 2024. [PMID: 38442041 DOI: 10.1021/acs.jproteome.3c00912] [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] [Indexed: 03/07/2024]
Abstract
Post-translational modifications (PTMs) have been extensively studied in both eukaryotes and prokaryotes. Lysine acetylation, originally thought to be a rare occurrence in bacteria, is now recognized as a prevalent and important PTM in more than 50 species. This expansion in interest in bacterial PTMs became possible with the advancement of mass spectrometry technology and improved reagents such as acyl-modification specific antibodies. In this Review, we discuss how mass spectrometry-based proteomic studies of lysine acetylation and other acyl modifications have contributed to our understanding of bacterial physiology, focusing on recently published studies from 2018 to 2023. We begin with a discussion of approaches used to study bacterial PTMs. Next, we discuss newly characterized acylomes, including acetylomes, succinylomes, and malonylomes, in different bacterial species. In addition, we examine proteomic contributions to our understanding of bacterial virulence and biofilm formation. Finally, we discuss the contributions of mass spectrometry to our understanding of the mechanisms of acetylation, both enzymatic and nonenzymatic. We end with a discussion of the current state of the field and possible future research avenues to explore.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Rachel A Carr
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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Helms A, Brodbelt JS. Mass Spectrometry Strategies for O-Glycoproteomics. Cells 2024; 13:394. [PMID: 38474358 DOI: 10.3390/cells13050394] [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: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Glycoproteomics has accelerated in recent decades owing to numerous innovations in the analytical workflow. In particular, new mass spectrometry strategies have contributed to inroads in O-glycoproteomics, a field that lags behind N-glycoproteomics due to several unique challenges associated with the complexity of O-glycosylation. This review will focus on progress in sample preparation, enrichment strategies, and MS/MS techniques for the identification and characterization of O-glycoproteins.
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Affiliation(s)
- Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
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Lermyte F. The need for open and FAIR data in top-down proteomics. Proteomics 2024; 24:e2300354. [PMID: 38088481 DOI: 10.1002/pmic.202300354] [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: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 02/15/2024]
Abstract
In recent years, there has been a tremendous evolution in the high-throughput, tandem mass spectrometry-based analysis of intact proteins, also known as top-down proteomics (TDP). Both hardware and software have developed to the point that the technique has largely entered the mainstream, and large-scale, ambitious, multi-laboratory initiatives have started to make their appearance in the literature. For this, however, more convenient and robust data sharing and reuse will be required. Walzer et al. have created TopDownApp, a customisable, open platform for visualisation and analysis of TDP data, which they hope will be a step in this direction. As they point out, other benefits of such data sharing and interoperability would include reanalysis of published datasets, as well as the prospect of using large amounts of data to train machine learning algorithms. In time, this work could prove to be a valuable resource in the move towards a future of greater TDP data findability, accessibility, interoperability and reusability.
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Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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Habeck T, Maciel EVS, Kretschmer K, Lermyte F. Charge site manipulation to enhance top-down fragmentation efficiency. Proteomics 2024; 24:e2300082. [PMID: 37043727 DOI: 10.1002/pmic.202300082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
In recent years, top-down mass spectrometry has become a widely used approach to study proteoforms; however, improving sequence coverage remains an important goal. Here, two different proteins, α-synuclein and bovine carbonic anhydrase, were subjected to top-down collision-induced dissociation (CID) after electrospray ionisation. Two high-boiling solvents, DMSO and propylene carbonate, were added to the protein solution in low concentration (2%) and the effects on the top-down fragmentation patterns of the proteins were systematically investigated. Each sample was measured in triplicate, which revealed highly reproducible differences in the top-down CID fragmentation patterns in the presence of a solution additive, even if the same precursor charge state was isolated in the quadrupole of the instrument. Further investigation supports the solution condition-dependent selective formation of different protonation site isomers as the underlying cause of these differences. Higher sequence coverage was often observed in the presence of additives, and the benefits of this approach became even more evident when datasets from different solution conditions were combined, as increases up to 35% in cleavage coverage were obtained. Overall, this approach therefore represents a promising opportunity to increase top-down fragmentation efficiency.
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Affiliation(s)
- Tanja Habeck
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Edvaldo Vasconcelos Soares Maciel
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Kevin Kretschmer
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Frederik Lermyte
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
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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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13
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Dowling P, Trollet C, Negroni E, Swandulla D, Ohlendieck K. How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction? Proteomes 2024; 12:4. [PMID: 38250815 PMCID: PMC10801633 DOI: 10.3390/proteomes12010004] [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: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Capucine Trollet
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Elisa Negroni
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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14
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Egbejiogu BC, Donnarumma F, Dong C, Murray KK. Infrared Laser Ablation and Capture of Biological Tissue. Methods Mol Biol 2024; 2817:9-18. [PMID: 38907143 DOI: 10.1007/978-1-0716-3934-4_2] [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: 06/23/2024]
Abstract
Sampling thin tissue sections with cellular precision can be accomplished using laser ablation microsampling for mass spectrometry analysis. In this work, the use of a pulsed mid-infrared (IR) laser for selecting small regions of interest (ROI) in tissue sections for offline liquid chromatography-tandem mass spectrometry (LC-MS/MS) is described. The laser is focused onto the tissue section, which is rastered as the laser is fired. The ablated tissue is captured in a microwell array and processed in situ through reduction, alkylation, and digestion with a low liquid volume workflow. The resulting peptides from areas as small as 0.01 mm2 containing 5 ng of protein are analyzed for protein identification and quantification using offline LC-MS/MS.
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Affiliation(s)
| | | | - Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, USA.
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15
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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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16
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Po A, Eyers CE. Top-Down Proteomics and the Challenges of True Proteoform Characterization. J Proteome Res 2023; 22:3663-3675. [PMID: 37937372 PMCID: PMC10696603 DOI: 10.1021/acs.jproteome.3c00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Top-down proteomics (TDP) aims to identify and profile intact protein forms (proteoforms) extracted from biological samples. True proteoform characterization requires that both the base protein sequence be defined and any mass shifts identified, ideally localizing their positions within the protein sequence. Being able to fully elucidate proteoform profiles lends insight into characterizing proteoform-unique roles, and is a crucial aspect of defining protein structure-function relationships and the specific roles of different (combinations of) protein modifications. However, defining and pinpointing protein post-translational modifications (PTMs) on intact proteins remains a challenge. Characterization of (heavily) modified proteins (>∼30 kDa) remains problematic, especially when they exist in a population of similarly modified, or kindred, proteoforms. This issue is compounded as the number of modifications increases, and thus the number of theoretical combinations. Here, we present our perspective on the challenges of analyzing kindred proteoform populations, focusing on annotation of protein modifications on an "average" protein. Furthermore, we discuss the technical requirements to obtain high quality fragmentation spectral data to robustly define site-specific PTMs, and the fact that this is tempered by the time requirements necessary to separate proteoforms in advance of mass spectrometry analysis.
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Affiliation(s)
- Allen Po
- Centre
for Proteome Research, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, Faculty of Health & Life
Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, Faculty of Health & Life
Sciences, University of Liverpool, Liverpool L69 7ZB, U.K.
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17
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Lippold S, Cadang L, Schlothauer T, Yang F. Internal Fragment Ions from Higher Energy Collision Dissociation Enable the Glycoform-Resolved Asn325 Deamidation Assessment of Antibodies by Middle-Down Mass Spectrometry. Anal Chem 2023; 95:16447-16452. [PMID: 37903404 DOI: 10.1021/acs.analchem.3c03015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
A major challenge in proteoform characterization is to obtain information on coexisting post-translational modifications (PTMs), which is lost in traditional bottom-up analysis. Middle-down approaches of antibodies provide a good balance of resolution, site-specificity, and proteoform heterogeneity to characterize individual proteoforms at subunit level. Currently, most middle-down studies focus on terminal fragment ions, which may not cover or resolve PTMs in the center of the sequence or with minor mass shifts such as deamidation, often a critical quality attribute for antibody drugs. Antibody glycosylation at Asn 297 and deamidation at Asn 325 are two important PTMs impacting the interaction with Fc gamma receptors and hence effector functions such as antibody-dependent cellular cytotoxicity. Here, we established a new middle-down workflow that uses internal fragment ions for the qualitative and quantitative assessment of a functional relevant deamidation site, Asn 325, through higher energy collision dissociation fragmentation of individual antibody glycoforms upon quadrupole isolation. We identified a signature internal fragment ion to resolve and estimate the relative abundances of deamidation of individual glycoforms in complex mixtures. Our proof-of-concept work demonstrates the feasibility to identify and quantify Asn 325 deamidation at the glycoform-resolved subunit level using internal fragment ions, which greatly advances the capabilities to study PTM dynamics by middle-down analysis.
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Affiliation(s)
- Steffen Lippold
- Protein Analytical Chemistry, Genentech, A Member of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lance Cadang
- Protein Analytical Chemistry, Genentech, A Member of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Tilman Schlothauer
- Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg 82377, Germany
| | - Feng Yang
- Protein Analytical Chemistry, Genentech, A Member of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
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18
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Koc MA, Wiles TA, Weinhold DC, Rightmyer S, Weaver AL, McDowell CT, Roder J, Asmellash S, Pestano GA, Roder H, Georgantas III RW. Molecular and translational biology of the blood-based VeriStrat® proteomic test used in cancer immunotherapy treatment guidance. J Mass Spectrom Adv Clin Lab 2023; 30:51-60. [PMID: 38074293 PMCID: PMC10709509 DOI: 10.1016/j.jmsacl.2023.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 03/09/2024] Open
Abstract
INTRODUCTION The VeriStrat® test (VS) is a blood-based assay that predicts a patient's response to therapy by analyzing eight features in a spectrum obtained from matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis of human serum and plasma. In a recent analysis of the INSIGHT clinical trial (NCT03289780), it was found that the VS labels, VS Good and VS Poor, can effectively predict the responsiveness of non-small cell lung cancer (NSCLC) patients to immune checkpoint inhibitor (ICI) therapy. However, while VS measures the intensities of spectral features using MALDI-TOF analysis, the specific proteoforms underlying these features have not been comprehensively identified. OBJECTIVES The objective of this study was to identify the proteoforms that are measured by VS. METHODS To resolve the features obtained from the low-resolution MALDI-TOF procedure used to acquire mass spectra for VS DeepMALDI® analysis of serum was employed. This technique allowed for the identification of finer peaks within these features. Additionally, a combination of reversed-phase fractionation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was then used to identify the proteoforms associated with these peaks. RESULTS The analysis revealed that the primary constituents of the spectrum measured by VS are serum amyloid A1, serum amyloid A2, serum amyloid A4, C-reactive protein, and beta-2 microglobulin. CONCLUSION Proteoforms involved in host immunity were identified as significant components of these features. This newly acquired information improves our understanding of how VS can accurately predict patient response to therapy. It opens up additional studies that can expand our understanding even further.
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Affiliation(s)
| | | | - Daniel C. Weinhold
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Steven Rightmyer
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Amanda L. Weaver
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Colin T. McDowell
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Joanna Roder
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Senait Asmellash
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Gary A. Pestano
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
| | - Heinrich Roder
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, United States
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19
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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20
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Abdelkader Y, Perez-Davalos L, LeDuc R, Zahedi RP, Labouta HI. Omics approaches for the assessment of biological responses to nanoparticles. Adv Drug Deliv Rev 2023; 200:114992. [PMID: 37414362 DOI: 10.1016/j.addr.2023.114992] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Nanotechnology has enabled the development of innovative therapeutics, diagnostics, and drug delivery systems. Nanoparticles (NPs) can influence gene expression, protein synthesis, cell cycle, metabolism, and other subcellular processes. While conventional methods have limitations in characterizing responses to NPs, omics approaches can analyze complete sets of molecular entities that change upon exposure to NPs. This review discusses key omics approaches, namely transcriptomics, proteomics, metabolomics, lipidomics and multi-omics, applied to the assessment of biological responses to NPs. Fundamental concepts and analytical methods used for each approach are presented, as well as good practices for omics experiments. Bioinformatics tools are essential to analyze, interpret and visualize large omics data, and to correlate observations in different molecular layers. The authors envision that conducting interdisciplinary multi-omics analyses in future nanomedicine studies will reveal integrated cell responses to NPs at different omics levels, and the incorporation of omics into the evaluation of targeted delivery, efficacy, and safety will improve the development of nanomedicine therapies.
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Affiliation(s)
- Yasmin Abdelkader
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St., Cairo 12622, Egypt
| | - Luis Perez-Davalos
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada
| | - Richard LeDuc
- Children's Hospital Research Institute of Manitoba, 513 - 715 McDermot Av. W, Winnipeg, Manitoba R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada
| | - Rene P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada; Department of Internal Medicine, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; CancerCare Manitoba Research Institute, 675 McDermot Av., Manitoba R3E 0V9, Canada
| | - Hagar I Labouta
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, Ontario M5S 3M2, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S 3G9, Canada; Faculty of Pharmacy, Alexandria University, 1 Khartoum Square, Azarita, Alexandria, Egypt, 21521.
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21
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Yan M, Zheng H, Yan R, Lang L, Wang Q, Xiao B, Zhang D, Lin H, Jia Y, Pan S, Chen Q. Vinculin Identified as a Potential Biomarker in Hand-Arm Vibration Syndrome Based on iTRAQ and LC-MS/MS-Based Proteomic Analysis. J Proteome Res 2023; 22:2714-2726. [PMID: 37437295 PMCID: PMC10408646 DOI: 10.1021/acs.jproteome.3c00277] [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] [Indexed: 07/14/2023]
Abstract
Local vibration can induce vascular injuries, one example is the hand-arm vibration syndrome (HAVS) caused by hand-transmitted vibration (HTV). Little is known about the molecular mechanism of HAVS-induced vascular injuries. Herein, the iTRAQ (isobaric tags for relative and absolute quantitation) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was applied to conduct the quantitative proteomic analysis of plasma from specimens with HTV exposure or HAVS diagnosis. Overall, 726 proteins were identified in iTRAQ. 37 proteins upregulated and 43 downregulated in HAVS. Moreover, 37 upregulated and 40 downregulated when comparing severe HAVS and mild HAVS. Among them, Vinculin (VCL) was found to be downregulated in the whole process of HAVS. The concentration of vinculin was further verified by ELISA, and the results suggested that the proteomics data was reliable. Bioinformative analyses were used, and those proteins mainly engaged in specific biological processes like binding, focal adhesion, and integrins. The potential of vinculin application in HAVS diagnosis was validated by the receiver operating characteristic curve.
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Affiliation(s)
- Maosheng Yan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Hanjun Zheng
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Rong Yan
- The
Centers for Disease Control and Prevention of Haizhu District, Guangzhou, Guangdong 510230, China
| | - Li Lang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Qia Wang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Bin Xiao
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Danying Zhang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Hansheng Lin
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Yanxia Jia
- Department
of Public Health, Shanxi Medical University, Tai Yuan, Shanxi 030000, China
| | - Siyu Pan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
| | - Qingsong Chen
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
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22
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Dowling P, Gargan S, Zweyer M, Swandulla D, Ohlendieck K. Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy. Biomolecules 2023; 13:1108. [PMID: 37509144 PMCID: PMC10377647 DOI: 10.3390/biom13071108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The progressive degeneration of the skeletal musculature in Duchenne muscular dystrophy is accompanied by reactive myofibrosis, fat substitution, and chronic inflammation. Fibrotic changes and reduced tissue elasticity correlate with the loss in motor function in this X-chromosomal disorder. Thus, although dystrophinopathies are due to primary abnormalities in the DMD gene causing the almost-complete absence of the cytoskeletal Dp427-M isoform of dystrophin in voluntary muscles, the excessive accumulation of extracellular matrix proteins presents a key histopathological hallmark of muscular dystrophy. Animal model research has been instrumental in the characterization of dystrophic muscles and has contributed to a better understanding of the complex pathogenesis of dystrophinopathies, the discovery of new disease biomarkers, and the testing of novel therapeutic strategies. In this article, we review how mass-spectrometry-based proteomics can be used to study changes in key components of the endomysium, perimysium, and epimysium, such as collagens, proteoglycans, matricellular proteins, and adhesion receptors. The mdx-4cv mouse diaphragm displays severe myofibrosis, making it an ideal model system for large-scale surveys of systematic alterations in the matrisome of dystrophic fibers. Novel biomarkers of myofibrosis can now be tested for their appropriateness in the preclinical and clinical setting as diagnostic, pharmacodynamic, prognostic, and/or therapeutic monitoring indicators.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, German Center for Neurodegenerative Diseases, University of Bonn, D53127 Bonn, Germany
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
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23
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Nimer RM, Abdel Rahman AM. Recent advances in proteomic-based diagnostics of cystic fibrosis. Expert Rev Proteomics 2023; 20:151-169. [PMID: 37766616 DOI: 10.1080/14789450.2023.2258282] [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: 01/03/2023] [Accepted: 07/06/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF. AREAS COVERED We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers. EXPERT OPINION Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.
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Affiliation(s)
- Refat M Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Anas M Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, Saudi Arabia
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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24
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Dowling P, Swandulla D, Ohlendieck K. Biochemical and proteomic insights into sarcoplasmic reticulum Ca 2+-ATPase complexes in skeletal muscles. Expert Rev Proteomics 2023; 20:125-142. [PMID: 37668143 DOI: 10.1080/14789450.2023.2255743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023]
Abstract
INTRODUCTION Skeletal muscles contain large numbers of high-molecular-mass protein complexes in elaborate membrane systems. Integral membrane proteins are involved in diverse cellular functions including the regulation of ion handling, membrane homeostasis, energy metabolism and force transmission. AREAS COVERED The proteomic profiling of membrane proteins and large protein assemblies in skeletal muscles are outlined in this article. This includes a critical overview of the main biochemical separation techniques and the mass spectrometric approaches taken to study membrane proteins. As an illustrative example of an analytically challenging large protein complex, the proteomic detection and characterization of the Ca2+-ATPase of the sarcoplasmic reticulum is discussed. The biological role of this large protein complex during normal muscle functioning, in the context of fiber type diversity and in relation to mechanisms of physiological adaptations and pathophysiological abnormalities is evaluated from a proteomics perspective. EXPERT OPINION Mass spectrometry-based muscle proteomics has decisively advanced the field of basic and applied myology. Although it is technically challenging to study membrane proteins, innovations in protein separation methodology in combination with sensitive mass spectrometry and improved systems bioinformatics has allowed the detailed proteomic detection and characterization of skeletal muscle membrane protein complexes, such as Ca2+-pump proteins of the sarcoplasmic reticulum.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth Kildare, Ireland
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Guo Y, Cupp‐Sutton KA, Zhao Z, Anjum S, Wu S. Multidimensional Separations in Top-Down Proteomics. ANALYTICAL SCIENCE ADVANCES 2023; 4:181-203. [PMID: 38188188 PMCID: PMC10769458 DOI: 10.1002/ansa.202300016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/21/2023] [Accepted: 05/01/2023] [Indexed: 01/09/2024]
Abstract
Top-down proteomics (TDP) identifies, quantifies, and characterizes proteins at the intact proteoform level in complex biological samples to understand proteoform function and cellular mechanisms. However, analyzing complex biological samples using TDP is still challenging due to high sample complexity and wide dynamic range. High-resolution separation methods are often applied prior to mass spectrometry (MS) analysis to decrease sample complexity and increase proteomics throughput. These separation methods, however, may not be efficient enough to characterize low abundance intact proteins in complex samples. As such, multidimensional separation techniques (combination of two or more separation methods with high orthogonality) have been developed and applied that demonstrate improved separation resolution and more comprehensive identification in TDP. A suite of multidimensional separation methods that couple various types of liquid chromatography (LC), capillary electrophoresis (CE), and/or gel electrophoresis-based separation approaches have been developed and applied in TDP to analyze complex biological samples. Here, we reviewed multidimensional separation strategies employed for TDP, summarized current applications, and discussed the gaps that may be addressed in the future.
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Affiliation(s)
- Yanting Guo
- Department of Chemistry and BiochemistryUniversity of OklahomaOklahomaNormanUSA
| | | | - Zhitao Zhao
- Department of Chemistry and BiochemistryUniversity of OklahomaOklahomaNormanUSA
| | - Samin Anjum
- Department of Chemistry and BiochemistryUniversity of OklahomaOklahomaNormanUSA
| | - Si Wu
- Department of Chemistry and BiochemistryUniversity of OklahomaOklahomaNormanUSA
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Rathore D, Marino MJ, Nita-Lazar A. Omics and systems view of innate immune pathways. Proteomics 2023; 23:e2200407. [PMID: 37269203 DOI: 10.1002/pmic.202200407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/16/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023]
Abstract
Multiomics approaches to studying systems biology are very powerful techniques that can elucidate changes in the genomic, transcriptomic, proteomic, and metabolomic levels within a cell type in response to an infection. These approaches are valuable for understanding the mechanisms behind disease pathogenesis and how the immune system responds to being challenged. With the emergence of the COVID-19 pandemic, the importance and utility of these tools have become evident in garnering a better understanding of the systems biology within the innate and adaptive immune response and for developing treatments and preventative measures for new and emerging pathogens that pose a threat to human health. In this review, we focus on state-of-the-art omics technologies within the scope of innate immunity.
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Affiliation(s)
- Deepali Rathore
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthew J Marino
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Fu X, Hong J, Zhai Y, Liu K, Xu W. Deep Bottom-up Proteomics Enabled by the Integration of Liquid-Phase Ion Trap. Anal Chem 2023. [PMID: 37367992 DOI: 10.1021/acs.analchem.3c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
In bottom-up proteomics, the complexity of the proteome requires advanced peptide separation and/or fractionation methods to acquire an in-depth understanding of protein profiles. Proposed earlier as a solution-phase ion manipulation device, liquid phase ion traps (LPITs) were used in front of mass spectrometers to accumulate target ions for improved detection sensitivity. In this work, an LPIT-reversed phase liquid chromatography-tandem mass spectrometry (LPIT-RPLC-MS/MS) platform was established for deep bottom-up proteomics. LPIT was used here as a robust and effective method for peptide fractionation, which also shows good reproducibility and sensitivity on both qualitative and quantitative levels. LPIT separates peptides based on their effective charges and hydrodynamic radii, which is orthogonal to that of RPLC. With excellent orthogonality, the integration of LPIT with RPLC-MS/MS could effectively increase the number of peptides and proteins being detected. When HeLa cells were analyzed, peptide and protein coverages were increased by ∼89.2% and 50.3%, respectively. With high efficiency and low cost, this LPIT-based peptide fraction method could potentially be used in routine deep bottom-up proteomics.
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Affiliation(s)
- Xinyan Fu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jie Hong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yanbing Zhai
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Kefu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410083, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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Xu T, Wang Q, Wang Q, Sun L. Coupling High-Field Asymmetric Waveform Ion Mobility Spectrometry with Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Top-Down Proteomics. Anal Chem 2023; 95:9497-9504. [PMID: 37254456 PMCID: PMC10540249 DOI: 10.1021/acs.analchem.3c00551] [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: 06/01/2023]
Abstract
Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has emerged as an essential technique for top-down proteomics (TDP), providing superior separation efficiency and high detection sensitivity for proteoform analysis. Here, we aimed to further enhance the performance of CZE-MS/MS for TDP via coupling online gas-phase proteoform fractionation using high-field asymmetric waveform ion mobility spectrometry (FAIMS). When the compensation voltage (CV) of FAIMS was changed from -50 to 30 V, the median mass of identified proteoforms increased from less than 10 kDa to about 30 kDa, suggesting that FAIMS can efficiently fractionate proteoforms by their size. CZE-FAIMS-MS/MS boosted the number of proteoform identifications from a yeast sample by nearly 3-fold relative to CZE-MS/MS alone. It particularly benefited the identification of relatively large proteoforms, improving the number of proteoforms in a mass range of 20-45 kDa by 6-fold compared to CZE-MS/MS alone. FAIMS fractionation gained nearly 20-fold better signal-to-noise ratios of randomly selected proteoforms than no FAIMS. We expect that CZE-FAIMS-MS/MS will be a useful tool for further advancing the sensitivity and coverage of TDP. This work shows the first example of coupling CE with ion mobility spectrometry (IMS) for TDP.
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Affiliation(s)
- Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, 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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Kline JT, Belford MW, Huang J, Greer JB, Bergen D, Fellers RT, Greer SM, Horn DM, Zabrouskov V, Huguet R, Boeser CL, Durbin KR, Fornelli L. Improved Label-Free Quantification of Intact Proteoforms Using Field Asymmetric Ion Mobility Spectrometry. Anal Chem 2023; 95:9090-9096. [PMID: 37252723 PMCID: PMC11149911 DOI: 10.1021/acs.analchem.3c01534] [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: 05/31/2023]
Abstract
The high-throughput quantification of intact proteoforms using a label-free approach is typically performed on proteins in the 0-30 kDa mass range extracted from whole cell or tissue lysates. Unfortunately, even when high-resolution separation of proteoforms is achieved by either high-performance liquid chromatography or capillary electrophoresis, the number of proteoforms that can be identified and quantified is inevitably limited by the inherent sample complexity. Here, we benchmark label-free quantification of proteoforms of Escherichia coli by applying gas-phase fractionation (GPF) via field asymmetric ion mobility spectrometry (FAIMS). Recent advances in Orbitrap instrumentation have enabled the acquisition of high-quality intact and fragmentation mass spectra without the need for averaging time-domain transients prior to Fourier transform. The resulting speed improvements allowed for the application of multiple FAIMS compensation voltages in the same liquid chromatography-tandem mass spectrometry experiment without increasing the overall data acquisition cycle. As a result, the application of FAIMS to label-free quantification based on intact mass spectra substantially increases the number of both identified and quantified proteoforms without penalizing quantification accuracy in comparison to traditional label-free experiments that do not adopt GPF.
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Affiliation(s)
- Jake T. Kline
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | | | - Jingjing Huang
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Joseph B. Greer
- Proteinaceous, Inc., Evanston, Illinois 60208, United States
| | - David Bergen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Ryan T. Fellers
- Proteinaceous, Inc., Evanston, Illinois 60208, United States
| | | | - David M. Horn
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | | | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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Faizi M, Fellers RT, Lu D, Drown BS, Jambhekar A, Lahav G, Kelleher NL, Gunawardena J. MSModDetector: A Tool for Detecting Mass Shifts and Post-Translational Modifications in Individual Ion Mass Spectrometry Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543961. [PMID: 37333327 PMCID: PMC10274720 DOI: 10.1101/2023.06.06.543961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Motivation Post-translational modifications (PTMs) on proteins regulate protein structures and functions. A single protein molecule can possess multiple modification sites that can accommodate various PTM types, leading to a variety of different patterns, or combinations of PTMs, on that protein. Different PTM patterns can give rise to distinct biological functions. To facilitate the study of multiple PTMs, top-down mass spectrometry (MS) has proven to be a useful tool to measure the mass of intact proteins, thereby enabling even widely separated PTMs to be assigned to the same protein molecule and allowing determination of how many PTMs are attached to a single protein. Results We developed a Python module called MSModDetector that studies PTM patterns from individual ion mass spectrometry (I MS) data. I MS is an intact protein mass spectrometry approach that generates true mass spectra without the need to infer charge states. The algorithm first detects and quantifies mass shifts for a protein of interest and subsequently infers potential PTM patterns using linear programming. The algorithm is evaluated on simulated I MS data and experimental I MS data for the tumor suppressor protein p53. We show that MSModDetector is a useful tool for comparing a protein's PTM pattern landscape across different conditions. An improved analysis of PTM patterns will enable a deeper understanding of PTM-regulated cellular processes. Availability The source code is available at https://github.com/marjanfaizi/MSModDetector together with the scripts used for analyses and to generate the figures presented in this study.
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Kim SS, Shin H, Ahn KG, Park YM, Kwon MC, Lim JM, Oh EK, Kim Y, Han SM, Noh DY. Quantifiable peptide library bridges the gap for proteomics based biomarker discovery and validation on breast cancer. Sci Rep 2023; 13:8991. [PMID: 37268731 DOI: 10.1038/s41598-023-36159-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023] Open
Abstract
Mass spectrometry (MS) based proteomics is widely used for biomarker discovery. However, often, most biomarker candidates from discovery are discarded during the validation processes. Such discrepancies between biomarker discovery and validation are caused by several factors, mainly due to the differences in analytical methodology and experimental conditions. Here, we generated a peptide library which allows discovery of biomarkers in the equal settings as the validation process, thereby making the transition from discovery to validation more robust and efficient. The peptide library initiated with a list of 3393 proteins detectable in the blood from public databases. For each protein, surrogate peptides favorable for detection in mass spectrometry was selected and synthesized. A total of 4683 synthesized peptides were spiked into neat serum and plasma samples to check their quantifiability in a 10 min liquid chromatography-MS/MS run time. This led to the PepQuant library, which is composed of 852 quantifiable peptides that cover 452 human blood proteins. Using the PepQuant library, we discovered 30 candidate biomarkers for breast cancer. Among the 30 candidates, nine biomarkers, FN1, VWF, PRG4, MMP9, CLU, PRDX6, PPBP, APOC1, and CHL1 were validated. By combining the quantification values of these markers, we generated a machine learning model predicting breast cancer, showing an average area under the curve of 0.9105 for the receiver operating characteristic curve.
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Affiliation(s)
- Sung-Soo Kim
- Manufacturing and Technology Division, Bertis Inc., Hungdeok 1-Ro, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 16954, Republic of Korea
- Bio Convergence Research Institute, Bertis Inc., Heungdeok 1-Ro, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 16954, Republic of Korea
| | - HyeonSeok Shin
- Bio Convergence Research Institute, Bertis Inc., Heungdeok 1-Ro, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 16954, Republic of Korea
| | - Kyung-Geun Ahn
- Manufacturing and Technology Division, Bertis Inc., Hungdeok 1-Ro, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 16954, Republic of Korea
| | - Young-Min Park
- Manufacturing and Technology Division, Bertis Inc., Hungdeok 1-Ro, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 16954, Republic of Korea
| | - Min-Chul Kwon
- Manufacturing and Technology Division, Bertis Inc., Hungdeok 1-Ro, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 16954, Republic of Korea
| | - Jae-Min Lim
- Manufacturing and Technology Division, Bertis Inc., Hungdeok 1-Ro, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 16954, Republic of Korea
| | - Eun-Kyung Oh
- Manufacturing and Technology Division, Bertis Inc., Hungdeok 1-Ro, Giheung-Gu, Yongin-Si, Gyeonggi-Do, 16954, Republic of Korea
| | - Yumi Kim
- Department of Surgery, CHA Gangnam Medical Center, CHA University School of Medicine, 566, Nonhyeon-ro, Gangnam-gu, Seoul, 06135, Republic of Korea
| | - Seung-Man Han
- Bertis Inc., 172, Dolma-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 13605, Republic of Korea
| | - Dong-Young Noh
- Department of Surgery, CHA Gangnam Medical Center, CHA University School of Medicine, 566, Nonhyeon-ro, Gangnam-gu, Seoul, 06135, Republic of Korea.
- Bertis Inc., 172, Dolma-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 13605, Republic of Korea.
- Seoul National University College of Medicine, 103 Daehak-Ro, Seoul, 03080, Republic of Korea.
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Zhang P, Wang M, Zhou T, Chen D. SeqWiz: a modularized toolkit for next-generation protein sequence database management and analysis. BMC Bioinformatics 2023; 24:201. [PMID: 37194023 DOI: 10.1186/s12859-023-05334-9] [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: 12/07/2021] [Accepted: 05/11/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Current proteomic technologies are fast-evolving to uncover the complex features of sequence processes, variations and modifications. Thus, protein sequence database and the corresponding softwares should also be improved to solve this issue. RESULTS We developed a state-of-the-art toolkit (SeqWiz) for constructing next-generation sequence databases and performing proteomic-centric sequence analyses. First, we proposed two derived data formats: SQPD (a well-structured and high-performance local sequence database based on SQLite), and SET (an associated list of selected entries based on JSON). The SQPD format follows the basic standards of the emerging PEFF format, which also aims to facilitate the search of complex proteoform. The SET format is designed for generating subsets with with high-efficiency. These formats are shown to greatly outperform the conventional FASTA or PEFF formats in time and resource consumption. Then, we mainly focused on the UniProt knowledgebase and developed a collection of open-source tools and basic modules for retrieving species-specific databases, formats conversion, sequence generation, sequence filter, and sequence analysis. These tools are implemented by using the Python language and licensed under the GNU General Public Licence V3. The source codes and distributions are freely available at GitHub ( https://github.com/fountao/protwiz/tree/main/seqwiz ). CONCLUSIONS SeqWiz is designed to be a collection of modularized tools, which is friendly to both end-users for preparing easy-to-use sequence databases as well as bioinformaticians for performing downstream sequence analysis. Besides the novel formats, it also provides compatible functions for handling the traditional text based FASTA or PEFF formats. We believe that SeqWiz will promote the implementing of complementary proteomics for data renewal and proteoform analysis to achieve precision proteomics. Additionally, it can also drive the improvement of proteomic standardization and the development of next-generation proteomic softwares.
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Affiliation(s)
- Ping Zhang
- Research Institute for Reproductive Medicine and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China
| | - Min Wang
- Research Institute for Reproductive Medicine and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China
| | - Tao Zhou
- Research Institute for Reproductive Medicine and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China.
- Wuxi Maternity and Child Health Care Hospital, Wuxi School of Medicine, Jiangnan University, Wuxi, China.
| | - Daozhen Chen
- Research Institute for Reproductive Medicine and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China.
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Naryzhny S. Quantitative Aspects of the Human Cell Proteome. Int J Mol Sci 2023; 24:ijms24108524. [PMID: 37239870 DOI: 10.3390/ijms24108524] [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: 04/06/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The number and identity of proteins and proteoforms presented in a single human cell (a cellular proteome) are fundamental biological questions. The answers can be found with sophisticated and sensitive proteomics methods, including advanced mass spectrometry (MS) coupled with separation by gel electrophoresis and chromatography. So far, bioinformatics and experimental approaches have been applied to quantitate the complexity of the human proteome. This review analyzed the quantitative information obtained from several large-scale panoramic experiments in which high-resolution mass spectrometry-based proteomics in combination with liquid chromatography or two-dimensional gel electrophoresis (2DE) were used to evaluate the cellular proteome. It is important that even though all these experiments were performed in different labs using different equipment and calculation algorithms, the main conclusion about the distribution of proteome components (proteins or proteoforms) was basically the same for all human tissues or cells. It follows Zipf's law and has a formula N = A/x, where N is the number of proteoforms, A is a coefficient, and x is the limit of proteoform detection in terms of abundance.
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Affiliation(s)
- Stanislav Naryzhny
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10, 119121 Moscow, Russia
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center "Kurchatov Institute", 188300 Gatchina, Russia
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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 2023. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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de Jong E, Kocer A. Current Methods for Identifying Plasma Membrane Proteins as Cancer Biomarkers. MEMBRANES 2023; 13:409. [PMID: 37103836 PMCID: PMC10142483 DOI: 10.3390/membranes13040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
Plasma membrane proteins are a special class of biomolecules present on the cellular membrane. They provide the transport of ions, small molecules, and water in response to internal and external signals, define a cell's immunological identity, and facilitate intra- and intercellular communication. Since they are vital to almost all cellular functions, their mutants, or aberrant expression is linked to many diseases, including cancer, where they are a part of cancer cell-specific molecular signatures and phenotypes. In addition, their surface-exposed domains make them exciting biomarkers for targeting by imaging agents and drugs. This review looks at the challenges in identifying cancer-related cell membrane proteins and the current methodologies that solve most of the challenges. We classified the methodologies as biased, i.e., search cells for the presence of already known membrane proteins. Second, we discuss the unbiased methods that can identify proteins without prior knowledge of what they are. Finally, we discuss the potential impact of membrane proteins on the early detection and treatment of cancer.
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Yang M, Unsihuay D, Hu H, Nguele Meke F, Qu Z, Zhang ZY, Laskin J. Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. Anal Chem 2023; 95:5214-5222. [PMID: 36917636 DOI: 10.1021/acs.analchem.2c04795] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool for label-free mapping of the spatial distribution of proteins in biological tissues. We have previously demonstrated imaging of individual proteoforms in biological tissues using nanospray desorption electrospray ionization (nano-DESI), an ambient liquid extraction-based MSI technique. Nano-DESI MSI generates multiply charged protein ions, which is advantageous for their identification using top-down proteomics analysis. In this study, we demonstrate proteoform mapping in biological tissues with a spatial resolution down to 7 μm using nano-DESI MSI. A substantial decrease in protein signals observed in high-spatial-resolution MSI makes these experiments challenging. We have enhanced the sensitivity of nano-DESI MSI experiments by optimizing the design of the capillary-based probe and the thickness of the tissue section. In addition, we demonstrate that oversampling may be used to further improve spatial resolution at little or no expense to sensitivity. These developments represent a new step in MSI-based spatial proteomics, which complements targeted imaging modalities widely used for studying biological systems.
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Affiliation(s)
- Manxi Yang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Daisy Unsihuay
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hang Hu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Frederick Nguele Meke
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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37
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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. MASS SPECTROMETRY REVIEWS 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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38
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Qin J, Guo J, Tang G, Li L, Yao SQ. Multiplex Identification of Post-Translational Modifications at Point-of-Care by Deep Learning-Assisted Hydrogel Sensors. Angew Chem Int Ed Engl 2023; 62:e202218412. [PMID: 36815677 DOI: 10.1002/anie.202218412] [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: 12/13/2022] [Revised: 02/02/2023] [Accepted: 02/23/2023] [Indexed: 02/24/2023]
Abstract
Multiplex detection of protein post-translational modifications (PTMs), especially at point-of-care, is of great significance in cancer diagnosis. Herein, we report a machine learning-assisted photonic crystal hydrogel (PCH) sensor for multiplex detection of PTMs. With closely-related PCH sensors microfabricated on a single chip, our design achieved not only rapid screening of PTMs at specific protein sites by using only naked eyes/cellphone, but also the feasibility of real-time monitoring of phosphorylation reactions. By taking advantage of multiplex sensor chips and a neural network algorithm, accurate prediction of PTMs by both their types and concentrations was enabled. This approach was ultimately used to detect and differentiate up/down regulation of different phosphorylation sites within the same protein in live mammalian cells. Our developed method thus holds potential for POC identification of various PTMs in early-stage diagnosis of protein-related diseases.
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Affiliation(s)
- Junjie Qin
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Jia Guo
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, Fujian, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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39
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Liu X, Li N. New thoughts and findings on invasion and metastasis of pancreatic ductal adenocarcinoma (PDAC) from comparative proteomics: multi-target therapy. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023:10.1007/s12094-023-03106-8. [PMID: 36745340 DOI: 10.1007/s12094-023-03106-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/28/2023] [Indexed: 02/07/2023]
Abstract
As one of the most aggressive malignant tumors, pancreatic ductal adenocarcinoma (PDAC) ranks as the fourth cancer-related mortality in the world. The extremely low survival rate is closely related to early invasion and distant metastasis. However, effective target therapy for weakening its malignant behavior remains limited. Over the past decades, many proteins correlating with invasion and metastasis of PDAC have been discovered using proteomics. The discovery of these proteins gives us a deeper understanding of the invasive and migratory processes of PDAC. This review is a systemic integration of these proteomics findings over the past 10 years. The discovered proteins were typically associated with the glycolytic process, hypoxic microenvironment, post-translational modification, extracellular matrix, exosomes, cancer stem cells, and immune escape. Some proteins were found to have multiple functions, and, cooperation between different proteins in the invasive and metastatic processes was found. This cooperation, and not just single protein function, may play a more significant role in the poor prognosis of PDAC. Therefore, multi-target therapy against these cooperative networks should be a primary choice in the future.
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Affiliation(s)
- Xinlu Liu
- 1st Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Na Li
- Department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China.
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40
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Popovic Z, Anderson LC, Zhang X, Butcher DS, Blakney GT, Zubarev RA, Marshall AG. Analysis of Isotopically Depleted Proteins Derived from Escherichia coli and Caenorhabditis elegans Cell Lines by Liquid Chromatography 21 T Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:137-144. [PMID: 36656140 DOI: 10.1021/jasms.2c00242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Protein mass measurement by mass spectrometry is complicated by wide isotopic distributions that result from incorporation of heavy isotopes of C, H, N, O, and S, thereby limiting signal-to-noise ratio (SNR) and accurate intact mass determination, particularly for larger proteins [Fenselau et al. Anal. Chem. 1983, 55 (2), 353-356]. Observation of the monoisotopic mass-to-charge ratio (m/z) is the simplest and most accurate way to determine intact protein mass, but as mass increases, the relative abundance of the monoisotopic peak becomes so low that it is often undetectable. Here, we used an isotopically depleted growth medium to culture bacterial cells (Escherichia coli), resulting in isotopically depleted proteins. Isotopically depleted proteins show increased sequence coverage, mass measurement accuracy, and increased S/N of the monoisotopic peak by Fourier transform ion cyclotron resonance mass spectrometry analysis. We then grew Caenorhabditis elegans cells in a medium containing living isotopically depleted E. coli cells, thereby producing the first isotopically depleted eukaryotic proteins. This is the first time isotopic depletion has been implemented for four isotopes (1H, 12C, 14N, and 16O), resulting in the highest degree of depletion ever used for protein analysis and further improving MS analysis.
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Affiliation(s)
- Zeljka Popovic
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Xuepei Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavagen 1, Solna, 171 77 Stockholm, Sweden
| | - David S Butcher
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Greg T Blakney
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Roman A Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavagen 1, Solna, 171 77 Stockholm, Sweden
| | - Alan G Marshall
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
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Abstract
Proteins are the key biological actors within cells, driving many biological processes integral to both healthy and diseased states. Understanding the depth of complexity represented within the proteome is crucial to our scientific understanding of cellular biology and to provide disease specific insights for clinical applications. Mass spectrometry-based proteomics is the premier method for proteome analysis, with the ability to both identify and quantify proteins. Although proteomics continues to grow as a robust field of bioanalytical chemistry, advances are still necessary to enable a more comprehensive view of the proteome. In this review, we provide a broad overview of mass spectrometry-based proteomics in general, and highlight four developing areas of bottom-up proteomics: (1) protein inference, (2) alternative proteases, (3) sample-specific databases and (4) post-translational modification discovery.
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Affiliation(s)
- Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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42
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Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics. PLoS Comput Biol 2023; 19:e1010457. [PMID: 36668672 PMCID: PMC9891523 DOI: 10.1371/journal.pcbi.1010457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/01/2023] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Generating and analyzing overlapping peptides through multienzymatic digestion is an efficient procedure for de novo protein using from bottom-up mass spectrometry (MS). Despite improved instrumentation and software, de novo MS data analysis remains challenging. In recent years, deep learning models have represented a performance breakthrough. Incorporating that technology into de novo protein sequencing workflows require machine-learning models capable of handling highly diverse MS data. In this study, we analyzed the requirements for assembling such generalizable deep learning models by systemcally varying the composition and size of the training set. We assessed the generated models' performances using two test sets composed of peptides originating from the multienzyme digestion of samples from various species. The peptide recall values on the test sets showed that the deep learning models generated from a collection of highly N- and C-termini diverse peptides generalized 76% more over the termini-restricted ones. Moreover, expanding the training set's size by adding peptides from the multienzymatic digestion with five proteases of several species samples led to a 2-3 fold generalizability gain. Furthermore, we tested the applicability of these multienzyme deep learning (MEM) models by fully de novo sequencing the heavy and light monomeric chains of five commercial antibodies (mAbs). MEMs extracted over 10000 matching and overlapped peptides across six different proteases mAb samples, achieving a 100% sequence coverage for 8 of the ten polypeptide chains. We foretell that the MEMs' proven improvements to de novo analysis will positively impact several applications, such as analyzing samples of high complexity, unknown nature, or the peptidomics field.
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43
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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44
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Guo Y, Chowdhury T, Seshadri M, Cupp-Sutton KA, Wang Q, Yu D, Wu S. Optimization of Higher-Energy Collisional Dissociation Fragmentation Energy for Intact Protein-Level Tandem Mass Tag Labeling. J Proteome Res 2023; 22:1406-1418. [PMID: 36603205 PMCID: PMC10164041 DOI: 10.1021/acs.jproteome.2c00549] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Isobaric chemical tag labeling (e.g., TMT) is a commonly used approach in quantitative proteomics, and quantification is enabled through detection of low-mass reporter ions generated after MS2 fragmentation. Recently, we have introduced and optimized an intact protein-level TMT labeling platform that demonstrated >90% labeling efficiency in complex samples with top-down proteomics. Higher-energy collisional dissociation (HCD) is commonly utilized for isobaric tag-labeled peptide fragmentation because it produces accurate reporter ion intensities and avoids loss of low mass ions. HCD energies have been optimized for isobaric tag labeled-peptides but have not been systematically evaluated for isobaric tag-labeled intact proteins. In this study, we report a systematic evaluation of normalized HCD fragmentation energies (NCEs) on TMT-labeled HeLa cell lysate using top-down proteomics. Our results suggested that reporter ions often result in higher ion intensities at higher NCEs. Optimal fragmentation of intact proteins for identification, however, required relatively lower NCE. We further demonstrated that a stepped NCE scheme with energies from 30% to 50% resulted in optimal quantification and identification of TMT-labeled HeLa proteins. These parameters resulted in an average reporter ion intensity of ∼4E4 and average proteoform spectrum matches (PrSMs) of >1000 per RPLC-MS/MS run with a 1% false discovery rate (FDR) cutoff.
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Affiliation(s)
- Yanting Guo
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Trishika Chowdhury
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Meena Seshadri
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Qingyu Wang
- School of Meteorology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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45
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Liang Y, Zhang L, Zhang Y. Chromatographic separation of peptides and proteins for characterization of proteomes. Chem Commun (Camb) 2023; 59:270-281. [PMID: 36504223 DOI: 10.1039/d2cc05568f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Characterization of proteomes aims to comprehensively characterize proteins in cells or tissues via two main strategies: (1) bottom-up strategy based on the separation and identification of enzymatic peptides; (2) top-down strategy based on the separation and identification of intact proteins. However, it is challenged by the high complexity of proteomes. Consequently, the improvements in peptide and protein separation technologies for simplifying the sample should be critical. In this feature article, separation columns for peptide and protein separation were introduced, and peptide separation technologies for bottom-up proteomic analysis as well as protein separation technologies for top-down proteomic analysis were summarized. The achievement, recent development, limitation and future trends are discussed. Besides, the outlook on challenges and future directions of chromatographic separation in the field of proteomics was also presented.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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46
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Lignieres L, Legros V, Khelil M, Senecaut N, Lauber MA, Camadro JM, Chevreux G. Capillary liquid chromatography coupled with mass spectrometry for analysis of nanogram protein quantities on a wide-pore superficially porous particle column in top-down proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1214:123566. [PMID: 36516651 DOI: 10.1016/j.jchromb.2022.123566] [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: 10/06/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
In top-down proteomics experiments, intact protein ions are subjected to gas-phase fragmentation for MS analysis without prior digestion. This approach is used to characterize post-translational modifications and clipped forms of proteins, avoids several "inference" problems associated with bottom-up proteomics, and is well suited to the study of proteoforms. In the past decade, top-down proteomics has progressed rapidly, taking advantage of MS instrumentation improvements and the efforts of pioneering groups working to improve sample handling and data processing. The potential of this technology has been established through its successful use in a number of important biological studies. However, many challenges remain to be addressed like improving protein separation capabilities such that it might become possible to expand the dynamic range of whole proteome analysis, address co-elution and convoluted mass spectral data, and aid final data processing from peak identification to quantification. In this study, we investigated the use of a wide-pore silica-based superficially porous media with a high coverage phenyl bonding, commercially packed into customized capillary columns for the purpose of top-down proteomics. Protein samples of increasing complexity were tested, namely subunit digests of a monoclonal antibody, components of purified histones and proteins extracted from eukaryotic ribosomes. High quality mass spectra were obtained from only 100 ng of protein sample while using difluoroacetic acid as an ion pairing agent to improve peak shape and chromatographic resolution. A peak width at half height of about 15 s for a 45 min gradient time was observed on a complex mixture giving an estimated peak capacity close to 100. Most importantly, efficient separations were obtained for highly diverse proteins and there was no need to make method specific adjustments, suggesting this is a highly versatile and easy-to-use setup for top-down proteomics.
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Affiliation(s)
- Laurent Lignieres
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Véronique Legros
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Manel Khelil
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Nicolas Senecaut
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Matthew A Lauber
- Waters Corporation, 34, Maple Street, Milford, MA 01757-3696, United States
| | | | - Guillaume Chevreux
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France.
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47
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Dowling P, Gargan S, Swandulla D, Ohlendieck K. Identification of Subproteomic Markers for Skeletal Muscle Profiling. Methods Mol Biol 2023; 2596:291-302. [PMID: 36378446 DOI: 10.1007/978-1-0716-2831-7_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The biochemical and cell biological profiling of contractile fiber types and subcellular structures plays a central role in basic and applied myology. Mass spectrometry-based proteomics presents an ideal approach for the systematic identification of proteomic and subproteomic markers. These representative components of fast versus slow muscle fibers and their subcellular fractions are highly useful for in-depth surveys of skeletal muscle adaptations to physiological challenges, as well as the improvement of diagnostic, prognostic, and therapy-monitoring methodologies in muscle pathology. This chapter outlines the identification of subproteomic markers for skeletal muscle profiling based on bottom-up and top-down approaches, including fluorescence two-dimensional difference gel electrophoresis (2D-DIGE).
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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48
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Abstract
The combination of large-scale protein separation techniques, sophisticated mass spectrometry, and systems bioinformatics has led to the establishment of proteomics as a distinct discipline within the wider field of protein biochemistry. Both discovery proteomics and targeted proteomics are widely used in biological and biomedical research, whereby the analytical approaches can be broadly divided into proteoform-centric top-down proteomics versus peptide-centric bottom-up proteomics. This chapter outlines the scientific value of top-down proteomics and describes how fluorescence two-dimensional difference gel electrophoresis can be combined with the systematic analysis of crucial post-translational modifications. The concept of on-membrane digestion following the electrophoretic transfer of proteins and the usefulness of comparative two-dimensional immunoblotting are discussed.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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49
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Sechovcová H, Rudl Kulhavá L, Fliegerová K, Killer J, Kopečný J. Advantages of label free method in comparison with 2DE proteomic analysis of Butyrivibrio fibrisolvens 3071 grown on different carbon sources. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2129477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hana Sechovcová
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | | | - Kateřina Fliegerová
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
| | - Jiří Killer
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - Jan Kopečný
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
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50
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Seeing the complete picture: proteins in top-down mass spectrometry. Essays Biochem 2022; 67:283-300. [PMID: 36468679 DOI: 10.1042/ebc20220098] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Abstract
Top-down protein mass spectrometry can provide unique insights into protein sequence and structure, including precise proteoform identification and study of protein–ligand and protein–protein interactions. In contrast with the commonly applied bottom-up approach, top-down approaches do not include digestion of the protein of interest into small peptides, but instead rely on the ionization and subsequent fragmentation of intact proteins. As such, it is fundamentally the only way to fully characterize the composition of a proteoform. Here, we provide an overview of how a top-down protein mass spectrometry experiment is performed and point out recent applications from the literature to the reader. While some parts of the top-down workflow are broadly applicable, different research questions are best addressed with specific experimental designs. The most important divide is between studies that prioritize sequence information (i.e., proteoform identification) versus structural information (e.g., conformational studies, or mapping protein–protein or protein–ligand interactions). Another important consideration is whether to work under native or denaturing solution conditions, and the overall complexity of the sample also needs to be taken into account, as it determines whether (chromatographic) separation is required prior to MS analysis. In this review, we aim to provide enough information to support both newcomers and more experienced readers in the decision process of how to answer a potential research question most efficiently and to provide an overview of the methods that exist to answer these questions.
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