1
|
White MEH, Sinn LR, Jones DM, de Folter J, Aulakh SK, Wang Z, Flynn HR, Krüger L, Tober-Lau P, Demichev V, Kurth F, Mülleder M, Blanchard V, Messner CB, Ralser M. Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics. Nat Biomed Eng 2024; 8:233-247. [PMID: 37474612 DOI: 10.1038/s41551-023-01067-5] [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: 07/19/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.
Collapse
Affiliation(s)
- Matthew E H White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ludwig R Sinn
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Marc Jones
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Joost de Folter
- Software Engineering and Artificial Intelligence Technology Platform, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ziyue Wang
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Helen R Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lynn Krüger
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Mülleder
- Core Facility High-throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Véronique Blanchard
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Precision Proteomic Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland.
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
| |
Collapse
|
2
|
Geiszler DJ, Polasky DA, Yu F, Nesvizhskii AI. Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides. Nat Commun 2023; 14:4132. [PMID: 37438360 DOI: 10.1038/s41467-023-39828-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 06/23/2023] [Indexed: 07/14/2023] Open
Abstract
Post-translational modifications are an area of great interest in mass spectrometry-based proteomics, with a surge in methods to detect them in recent years. However, post-translational modifications can introduce complexity into proteomics searches by fragmenting in unexpected ways, ultimately hindering the detection of modified peptides. To address these deficiencies, we present a fully automated method to find diagnostic spectral features for any modification. The features can be incorporated into proteomics search engines to improve modified peptide recovery and localization. We show the utility of this approach by interrogating fragmentation patterns for a cysteine-reactive chemoproteomic probe, RNA-crosslinked peptides, sialic acid-containing glycopeptides, and ADP-ribosylated peptides. We also analyze the interactions between a diagnostic ion's intensity and its statistical properties. This method has been incorporated into the open-search annotation tool PTM-Shepherd and the FragPipe computational platform.
Collapse
Affiliation(s)
- Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
3
|
Varriale F, Tartaglione L, Zervou SK, Miles CO, Mazur-Marzec H, Triantis TM, Kaloudis T, Hiskia A, Dell'Aversano C. Untargeted and targeted LC-MS and data processing workflow for the comprehensive analysis of oligopeptides from cyanobacteria. CHEMOSPHERE 2023; 311:137012. [PMID: 36397634 DOI: 10.1016/j.chemosphere.2022.137012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/26/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Cyanobacteria produce a plethora of structurally diverse bioactive secondary metabolites, including cyanotoxins which pose a serious threat to humans and other living organisms worldwide. Currently, a wide variety of mass spectrometry-based methods for determination of microcystins (MCs), the most commonly occurring and studied class of cyanotoxins, have been developed and employed for research and monitoring purposes. The scarcity of commercially available reference materials, together with the ever-growing range of mass spectrometers and analytical approaches, make the accuracy of quantitative analyses a critical point to be carefully investigated in view of a reliable risk evaluation. This study reports, a comparative investigation of the qualitative and quantitative MCs profile obtained using targeted and untargeted liquid chromatography-mass spectrometry approaches for the analyses of cyanobacterial biomass from Lake Kastoria, Greece. Comparison of the total MCs content measured by the two approaches showed good correlation, with variations in the range of 3.8-13.2%. In addition, the implementation of an analytical workflow on a hybrid linear ion trap/orbitrap mass spectrometer is described, based on combining data-dependent acquisition and a powerful database of cyanobacterial metabolites (CyanoMetDB) for the annotation of known and discovery of new cyanopeptides. This untargeted strategy proved highly effective for the identification of MCs, microginins, anabaenopeptins, and micropeptins. The systematic interpretation of the acquired fragmentation patterns allowed the elucidation of two new MC structural variants, MC-PrhcysR and MC-Prhcys(O)R, and proposal of structures for two new microginins, isomeric cyanostatin B and MG 821A, and three isomeric micropeptins at m/z 846.4715, 846.4711 and 846.4723.
Collapse
Affiliation(s)
- Fabio Varriale
- University of Napoli Federico II, Department of Pharmacy, School of Medicine and Surgery, Via D. Montesano 49, 80131, Napoli, Italy
| | - Luciana Tartaglione
- University of Napoli Federico II, Department of Pharmacy, School of Medicine and Surgery, Via D. Montesano 49, 80131, Napoli, Italy; CoNISMa - National Inter-University Consortium for Marine Sciences, Piazzale Flaminio 9, 00196, Rome, Italy.
| | - Sevasti-Kiriaki Zervou
- Laboratory of Photo-Catalytic Processes and Environmental Chemistry, Institute of Nanoscience and Nanotechnology (INN), National Center for Scientific Research "Demokritos", Patriarchou Grigoriou E & 27 Neapoleos Str, 15341 Agia Paraskevi, Athens, Greece
| | - Christopher O Miles
- Biotoxin Metrology, National Research Council Canada, 1411 Oxford Street, Nova Scotia, Canada
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Poland
| | - Theodoros M Triantis
- Laboratory of Photo-Catalytic Processes and Environmental Chemistry, Institute of Nanoscience and Nanotechnology (INN), National Center for Scientific Research "Demokritos", Patriarchou Grigoriou E & 27 Neapoleos Str, 15341 Agia Paraskevi, Athens, Greece
| | - Triantafyllos Kaloudis
- Laboratory of Photo-Catalytic Processes and Environmental Chemistry, Institute of Nanoscience and Nanotechnology (INN), National Center for Scientific Research "Demokritos", Patriarchou Grigoriou E & 27 Neapoleos Str, 15341 Agia Paraskevi, Athens, Greece
| | - Anastasia Hiskia
- Laboratory of Photo-Catalytic Processes and Environmental Chemistry, Institute of Nanoscience and Nanotechnology (INN), National Center for Scientific Research "Demokritos", Patriarchou Grigoriou E & 27 Neapoleos Str, 15341 Agia Paraskevi, Athens, Greece
| | - Carmela Dell'Aversano
- University of Napoli Federico II, Department of Pharmacy, School of Medicine and Surgery, Via D. Montesano 49, 80131, Napoli, Italy; CoNISMa - National Inter-University Consortium for Marine Sciences, Piazzale Flaminio 9, 00196, Rome, Italy
| |
Collapse
|
4
|
Sigismondo G, Papageorgiou DN, Krijgsveld J. Cracking chromatin with proteomics: From chromatome to histone modifications. Proteomics 2022; 22:e2100206. [PMID: 35633285 DOI: 10.1002/pmic.202100206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Abstract
Chromatin is the assembly of genomic DNA and proteins packaged in the nucleus of eukaryotic cells, which together are crucial in regulating a plethora of cellular processes. Histones may be the best known class of protein constituents in chromatin, which are decorated by a range of post-translational modifications to recruit accessory proteins and protein complexes to execute specific functions, ranging from DNA compaction, repair, transcription and duplication, all in a dynamic fashion and depending on the cellular state. The key role of chromatin in cellular fitness is emphasized by the deregulation of chromatin determinants predisposing to different diseases, including cancer. For this reason, deep investigation of chromatin composition is fundamental to better understand cellular physiology. Proteomic approaches have played a crucial role to understand critical aspects of this complex interplay, benefiting from the ability to identify and quantify proteins and their modifications in an unbiased manner. This review gives an overview of the proteomic approaches that have been developed by combining mass spectrometry-based with tailored biochemical and genetic methods to examine overall protein make-up of chromatin, to characterize chromatin domains, to determine protein interactions, and to decipher the broad spectrum of histone modifications that represent the quintessence of chromatin function. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Gianluca Sigismondo
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany
| | - Dimitris N Papageorgiou
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
| |
Collapse
|
5
|
Massignani E, Giambruno R, Maniaci M, Nicosia L, Yadav A, Cuomo A, Raimondi F, Bonaldi T. ProMetheusDB: An In-Depth Analysis of the High-Quality Human Methyl-proteome. Mol Cell Proteomics 2022; 21:100243. [PMID: 35577067 PMCID: PMC9207298 DOI: 10.1016/j.mcpro.2022.100243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/22/2022] [Accepted: 05/11/2022] [Indexed: 01/01/2023] Open
Abstract
Protein arginine (R) methylation is a post-translational modification involved in various biological processes, such as RNA splicing, DNA repair, immune response, signal transduction, and tumor development. Although several advancements were made in the study of this modification by mass spectrometry, researchers still face the problem of a high false discovery rate. We present a dataset of high-quality methylations obtained from several different heavy methyl stable isotope labeling with amino acids in cell culture experiments analyzed with a machine learning–based tool and show that this model allows for improved high-confidence identification of real methyl-peptides. Overall, our results are consistent with the notion that protein R methylation modulates protein–RNA interactions and suggest a role in rewiring protein–protein interactions, for which we provide experimental evidence for a representative case (i.e., NONO [non-POU domain–containing octamer-binding protein]–paraspeckle component 1 [PSPC1]). Upon intersecting our R-methyl-sites dataset with the PhosphoSitePlus phosphorylation dataset, we observed that R methylation correlates differently with S/T-Y phosphorylation in response to various stimuli. Finally, we explored the application of heavy methyl stable isotope labeling with amino acids in cell culture to identify unconventional methylated residues and successfully identified novel histone methylation marks on serine 28 and threonine 32 of H3. The database generated, named ProMetheusDB, is freely accessible at https://bioserver.ieo.it/shiny/app/prometheusdb. hmSEEKER 2.0 identifies methyl-peptides from hmSILAC data through machine learning. Arginine methylation plays a role in modulating protein–protein interactions. Arginine methylations occur more frequently in proximity of phosphorylation sites. hmSEEKER 2.0 was used to identify methylations occurring on nonstandard amino acids.
Collapse
Affiliation(s)
- Enrico Massignani
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; European School of Molecular Medicine (SEMM), Milan, Italy
| | - Roberto Giambruno
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Center for Genomic Science of Istituto Italiano di Tecnologia at European School of Molecular Medicine, Istituto Italiano di Tecnologia, Milan, Italy; Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Marianna Maniaci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; European School of Molecular Medicine (SEMM), Milan, Italy
| | - Luciano Nicosia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Avinash Yadav
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Raimondi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Bio@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy.
| |
Collapse
|
6
|
Pabst M, Grouzdev DS, Lawson CE, Kleikamp HBC, de Ram C, Louwen R, Lin YM, Lücker S, van Loosdrecht MCM, Laureni M. A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium. THE ISME JOURNAL 2022; 16:346-357. [PMID: 34341504 PMCID: PMC8776859 DOI: 10.1038/s41396-021-01073-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
The enormous chemical diversity and strain variability of prokaryotic protein glycosylation makes their large-scale exploration exceptionally challenging. Therefore, despite the universal relevance of protein glycosylation across all domains of life, the understanding of their biological significance and the evolutionary forces shaping oligosaccharide structures remains highly limited. Here, we report on a newly established mass binning glycoproteomics approach that establishes the chemical identity of the carbohydrate components and performs untargeted exploration of prokaryotic oligosaccharides from large-scale proteomics data directly. We demonstrate our approach by exploring an enrichment culture of the globally relevant anaerobic ammonium-oxidizing bacterium Ca. Kuenenia stuttgartiensis. By doing so we resolve a remarkable array of oligosaccharides, which are produced by two seemingly unrelated biosynthetic routes, and which modify the same surface-layer protein simultaneously. More intriguingly, the investigated strain also accomplished modulation of highly specialized sugars, supposedly in response to its energy metabolism-the anaerobic oxidation of ammonium-which depends on the acquisition of substrates of opposite charges. Ultimately, we provide a systematic approach for the compositional exploration of prokaryotic protein glycosylation, and reveal a remarkable example for the evolution of complex oligosaccharides in bacteria.
Collapse
Affiliation(s)
- Martin Pabst
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | | | - Christopher E. Lawson
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA
| | - Hugo B. C. Kleikamp
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Carol de Ram
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Rogier Louwen
- grid.5645.2000000040459992XDepartment of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Yue Mei Lin
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mark C. M. van Loosdrecht
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Michele Laureni
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| |
Collapse
|
7
|
Jakobsson ME. Enzymology and significance of protein histidine methylation. J Biol Chem 2021; 297:101130. [PMID: 34461099 PMCID: PMC8446795 DOI: 10.1016/j.jbc.2021.101130] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Cells synthesize proteins using 20 standard amino acids and expand their biochemical repertoire through intricate enzyme-mediated post-translational modifications (PTMs). PTMs can either be static and represent protein editing events or be dynamically regulated as a part of a cellular response to specific stimuli. Protein histidine methylation (Hme) was an elusive PTM for over 5 decades and has only recently attracted considerable attention through discoveries concerning its enzymology, extent, and function. Here, we review the status of the Hme field and discuss the implications of Hme in physiological and cellular processes. We also review the experimental toolbox for analysis of Hme and discuss the strengths and weaknesses of different experimental approaches. The findings discussed in this review demonstrate that Hme is widespread across cells and tissues and functionally regulates key cellular processes such as cytoskeletal dynamics and protein translation. Collectively, the findings discussed here showcase Hme as a regulator of key cellular functions and highlight the regulation of this modification as an emerging field of biological research.
Collapse
|
8
|
Musiani D, Massignani E, Cuomo A, Yadav A, Bonaldi T. Biochemical and Computational Approaches for the Large-Scale Analysis of Protein Arginine Methylation by Mass Spectrometry. Curr Protein Pept Sci 2021; 21:725-739. [PMID: 32338214 DOI: 10.2174/1389203721666200426232531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/27/2022]
Abstract
The absence of efficient mass spectrometry-based approaches for the large-scale analysis of protein arginine methylation has hindered the understanding of its biological role, beyond the transcriptional regulation occurring through histone modification. In the last decade, however, several technological advances of both the biochemical methods for methylated polypeptide enrichment and the computational pipelines for MS data analysis have considerably boosted this research field, generating novel insights about the extent and role of this post-translational modification. Here, we offer an overview of state-of-the-art approaches for the high-confidence identification and accurate quantification of protein arginine methylation by high-resolution mass spectrometry methods, which comprise the development of both biochemical and bioinformatics methods. The further optimization and systematic application of these analytical solutions will lead to ground-breaking discoveries on the role of protein methylation in biological processes.
Collapse
Affiliation(s)
- Daniele Musiani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Avinash Yadav
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| |
Collapse
|
9
|
Huh S, Hwang D, Kim MS. Statistical Modeling for Enhancing the Discovery Power of Citrullination from Tandem Mass Spectrometry Data. Anal Chem 2020; 92:12975-12986. [PMID: 32876429 DOI: 10.1021/acs.analchem.0c01687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Citrullination is a post-translational modification implicated in various human diseases including rheumatoid arthritis, Alzheimer's disease, multiple sclerosis, and cancers. Due to a relatively low concentration of citrullinated proteins in the total proteome, confident identification of citrullinated proteome is challenging in mass spectrometry (MS)-based proteomic analysis. From these MS-based analyses, MS features that characterize citrullination, such as immonium ions (IMs) and neutral losses (NLs), called diagnostic ions, have been reported. However, there has been a lack of systematic approaches to comprehensively search for diagnostic ions and no statistical methods for the identification of citrullinated proteome based on these diagnostic ions. Here, we present a systematic approach to identify diagnostic IMs, internal ions (INTs), and NLs for citrullination from tandem mass (MS/MS) spectra. Diagnostic INTs mainly consisted of internal fragment ions for di- and tripeptides that contained two and three amino acids with at least one citrullinated arginine, respectively. A statistical logistic regression model was built for a confident assessment of citrullinated peptides that database searches identified (true positives) and prediction of citrullinated peptides that database searches failed to identify (false negatives) using the diagnostic IMs, INTs, and NLs. Applications of our model to complex global proteome data sets demonstrated the increased accuracy in the identification of citrullinated peptides, thereby enhancing the size and functional interpretation of citrullinated proteomes.
Collapse
Affiliation(s)
- Sunghyun Huh
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul 88026, Republic of Korea
| | - Min-Sik Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| |
Collapse
|
10
|
Mamani-Huanca M, Gradillas A, Gil de la Fuente A, López-Gonzálvez Á, Barbas C. Unveiling the Fragmentation Mechanisms of Modified Amino Acids as the Key for Their Targeted Identification. Anal Chem 2020; 92:4848-4857. [DOI: 10.1021/acs.analchem.9b04313] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maricruz Mamani-Huanca
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Alberto Gil de la Fuente
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
- Department of Information Technology, Escuela Politécnica Superior, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| |
Collapse
|
11
|
Renuse S, Madugundu AK, Jung JH, Byeon SK, Goldschmidt HL, Tahir R, Meyers D, Kim DI, Cutler J, Kim KP, Wu X, Huganir RL, Pandey A. Signature Fragment Ions of Biotinylated Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:394-404. [PMID: 31939678 PMCID: PMC7199424 DOI: 10.1021/jasms.9b00024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The use of biotin or biotin-containing reagents is an essential component of many protein purification and labeling technologies. Owing to its small size and high affinity to the avidin family of proteins, biotin is a versatile molecular handle that permits both enrichment and purity that is not easily achieved by other reagents. Traditionally, the use of biotinylation to enrich for proteins has not required the detection of the site of biotinylation. However, newer technologies for discovery of protein-protein interactions, such as APEX and BioID, as well as some of the click chemistry-based labeling approaches have underscored the importance of determining the exact residue that is modified by biotin. Anti-biotin antibody-based enrichment of biotinylated peptides (e.g., BioSITe) coupled to LC-MS/MS permit large-scale detection and localization of sites of biotinylation. As with any chemical modification of peptides, understanding the fragmentation patterns that result from biotin modification is essential to improving its detection by LC-MS/MS. Tandem mass spectra of biotinylated peptides has not yet been studied systematically. Here, we describe the various signature fragment ions generated with collision-induced dissociation of biotinylated peptides. We focused on biotin adducts attached to peptides generated by BioID and APEX experiments, including biotin, isotopically heavy biotin, and biotin-XX-phenol, a nonpermeable variant of biotin-phenol. We also highlight how the detection of biotinylated peptides in high-throughput studies poses certain computational challenges for accurate quantitation which need to be addressed. Our findings about signature fragment ions of biotinylated peptides should be helpful in the confirmation of biotinylation sites.
Collapse
Affiliation(s)
- Santosh Renuse
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Anil K. Madugundu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, Karnataka, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka India
| | - Jae Hun Jung
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, South Korea
| | - Seul Kee Byeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Hana L. Goldschmidt
- Solomon H. Snyder Department of Neuroscience, Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Raiha Tahir
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - David Meyers
- Synthetic Core Facility, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Dae In Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Jevon Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Pre-Doctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, South Korea
| | - Xinyan Wu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Richard L. Huganir
- Solomon H. Snyder Department of Neuroscience, Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka India
| |
Collapse
|
12
|
Zolg DP, Wilhelm M, Schmidt T, Médard G, Zerweck J, Knaute T, Wenschuh H, Reimer U, Schnatbaum K, Kuster B. ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides. Mol Cell Proteomics 2018; 17:1850-1863. [PMID: 29848782 PMCID: PMC6126394 DOI: 10.1074/mcp.tir118.000783] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/21/2018] [Indexed: 11/06/2022] Open
Abstract
The analysis of the post-translational modification (PTM) state of proteins using mass spectrometry-based bottom-up proteomic workflows has evolved into a powerful tool for the study of cellular regulatory events that are not directly encoded at the genome level. Besides frequently detected modifications such as phosphorylation, acetylation and ubiquitination, many low abundant or less frequently detected PTMs are known or postulated to serve important regulatory functions. To more broadly understand the LC-MS/MS characteristics of PTMs, we synthesized and analyzed ∼5,000 peptides representing 21 different naturally occurring modifications of lysine, arginine, proline and tyrosine side chains and their unmodified counterparts. The analysis identified changes in retention times, shifts of precursor charge states and differences in search engine scores between modifications. PTM-dependent changes in the fragmentation behavior were evaluated using eleven different fragmentation modes or collision energies. We also systematically investigated the formation of diagnostic ions or neutral losses for all PTMs, confirming 10 known and identifying 5 novel diagnostic ions for lysine modifications. To demonstrate the value of including diagnostic ions in database searching, we reprocessed a public data set of lysine crotonylation and showed that considering the diagnostic ions increases confidence in the identification of the modified peptides. To our knowledge, this constitutes the first broad and systematic analysis of the LC-MS/MS properties of common and rare PTMs using synthetic peptides, leading to direct applicable utility for bottom-up proteomic experiments.
Collapse
Affiliation(s)
- Daniel Paul Zolg
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tobias Schmidt
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Guillaume Médard
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | | | | | - Ulf Reimer
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Bernhard Kuster
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
- ¶Center for Integrated Protein Science Munich, Freising, Germany
- ‖Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| |
Collapse
|
13
|
Guo C, Guo XF, Zhao L, Chen DD, Wang J, Sun J. A Study on Immonium Ions and Immonium-Related Ions Depending on Different Collision Energies as Assessed by Q-TOF MS. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018040088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
14
|
Proteomic Analysis of Histone Variants and Their PTMs: Strategies and Pitfalls. Proteomes 2018; 6:proteomes6030029. [PMID: 29933573 PMCID: PMC6161106 DOI: 10.3390/proteomes6030029] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 12/14/2022] Open
Abstract
Epigenetic modifications contribute to the determination of cell fate and differentiation. The molecular mechanisms underlying histone variants and post-translational modifications (PTMs) have been studied in the contexts of development, differentiation, and disease. Antibody-based assays have classically been used to target PTMs, but these approaches fail to reveal combinatorial patterns of modifications. In addition, some histone variants are so similar to canonical histones that antibodies have difficulty distinguishing between these isoforms. Mass spectrometry (MS) has progressively developed as a powerful technology for the study of histone variants and their PTMs. Indeed, MS analyses highlighted exquisitely complex combinations of PTMs, suggesting “crosstalk” between them, and also revealed that PTM patterns are often variant-specific. Even though the sensitivity and acquisition speed of MS instruments have considerably increased alongside the development of computational tools for the study of multiple PTMs, it remains challenging to correctly describe the landscape of histone PTMs, and in particular to confidently assign modifications to specific amino acids. Here, we provide an inventory of MS-based strategies and of the pitfalls inherent to histone PTM and variant characterization, while stressing the complex interplay between PTMs and histone sequence variations. We will particularly illustrate the roles played by MS-based analyses in identifying and quantifying histone variants and modifications.
Collapse
|
15
|
Kwak HG, Suzuki T, Dohmae N. Global mapping of post-translational modifications on histone H3 variants in mouse testes. Biochem Biophys Rep 2017; 11:1-8. [PMID: 28955761 PMCID: PMC5614684 DOI: 10.1016/j.bbrep.2017.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/23/2017] [Indexed: 11/17/2022] Open
Abstract
Mass spectrometry (MS)-based characterization is important in proteomic research for verification of structural features and functional understanding of gene expression. Post-translational modifications (PTMs) such as methylation and acetylation have been reported to be associated with chromatin remodeling during spermatogenesis. Although antibody- and MS-based approaches have been applied for characterization of PTMs on H3 variants during spermatogenesis, variant-specific PTMs are still underexplored. We identified several lysine modifications in H3 variants, including testis-specific histone H3 (H3t), through their successful separation with MS-based strategy, based on differences in masses, retention times, and presence of immonium ions. Besides methylation and acetylation, we detected formylation as a novel PTM on H3 variants in mouse testes. These patterns were also observed in H3t. Our data provide high-throughput structural information about PTMs on H3 variants in mouse testes and show possible applications of this strategy in future proteomic studies on histone PTMs. Various post-translational modifications in histone H3 variants were characterized in the mouse testes. We specifically identified similar modified patterns based on immonium ions. Novel modified lysines in testis-specific H3 histone, H3t, were verified. Our approach will be helpful for the discovery of other novel or specific modifications during spermatogenesis.
Collapse
Key Words
- DTT, dithiothreitol
- ESI-TRAP, electrospray TRAP
- FDR, false discovery rate
- H2SO4, sulfuric acid
- HCD, high-energy collision dissociation
- HFBA, heptafluorobutyric acid
- HPLC, high performance liquid chromatography
- ISD, in source decay
- MALDI, matrix-assisted laser desorption/ionization
- MS, mass spectrometry
- Mass spectrometry
- PTMs, post-translational modifications
- Post-translational modification
- RP, reverse phase
- SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis
- Spermatogenesis
- TCA, trichloroacetic acid
- TFA, trifluoroacetic acid
- Testis-specific H3 histone
Collapse
|
16
|
Kim MS, Zhong J, Pandey A. Common errors in mass spectrometry-based analysis of post-translational modifications. Proteomics 2016; 16:700-14. [PMID: 26667783 DOI: 10.1002/pmic.201500355] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/05/2015] [Accepted: 12/08/2015] [Indexed: 12/29/2022]
Abstract
Mass spectrometry (MS) is a powerful tool to analyze complex mixtures of proteins in a high-throughput fashion. Proteome analysis has already become a routine task in biomedical research with the emergence of proteomics core facilities in most research institutions. Post-translational modifications (PTMs) represent a mechanism by which complex biological processes are orchestrated dynamically at the systems level. MS is rapidly becoming popular to discover new modifications and novel sites of known PTMs, revolutionizing the current understanding of diverse signaling pathways and biological processes. However, MS-based analysis of PTMs has its own caveats and pitfalls that can lead to erroneous conclusions. Here, we review the most common errors in MS-based PTM analyses with the goal of adopting strategies that maximize correct interpretation in the context of biological questions that are being addressed. Finally, we provide suggestions that should help mass spectrometrists, bioinformaticians and biologists to perform and interpret MS-based PTM analyses more accurately.
Collapse
Affiliation(s)
- Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Zhong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|