1
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Jiao F, Yu C, Wheat A, Chen L, Lih TSM, Zhang H, Huang L. DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples. J Proteome Res 2024. [PMID: 38334954 DOI: 10.1021/acs.jproteome.3c00832] [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: 02/10/2024]
Abstract
Protein-protein interactions (PPIs) are fundamental to understanding biological systems as protein complexes are the active molecular modules critical for carrying out cellular functions. Dysfunctional PPIs have been associated with various diseases including cancer. Systems-wide PPI analysis not only sheds light on pathological mechanisms, but also represents a paradigm in identifying potential therapeutic targets. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for defining endogenous PPIs of cellular networks. While proteome-wide studies have been performed in cell lysates, intact cells and tissues, applications of XL-MS in clinical samples have not been reported. In this study, we adopted a DSBSO-based in vivo XL-MS platform to map interaction landscapes from two breast cancer patient-derived xenograft (PDX) models. As a result, we have generated a PDX interaction network comprising 2,557 human proteins and identified interactions unique to breast cancer subtypes. Interestingly, most of the observed differences in PPIs correlated well with protein abundance changes determined by TMT-based proteome quantitation. Collectively, this work has demonstrated the feasibility of XL-MS analysis in clinical samples, and established an analytical workflow for tissue cross-linking that can be generalized for mapping PPIs from patient samples in the future to dissect disease-relevant cellular networks.
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Affiliation(s)
- Fenglong Jiao
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States
| | - Andrew Wheat
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Tung-Shing Mamie Lih
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States
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2
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Ruwolt M, Piazza I, Liu F. The potential of cross-linking mass spectrometry in the development of protein-protein interaction modulators. Curr Opin Struct Biol 2023; 82:102648. [PMID: 37423038 DOI: 10.1016/j.sbi.2023.102648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) can provide a wealth of information on endogenous protein-protein interaction (PPI) networks and protein binding interfaces. These features make XL-MS an attractive tool to support the development of PPI-targeting drugs. Though not yet widely used, applications of XL-MS to drug characterization are beginning to emerge. Here, we compare XL-MS to established structural proteomics methods in drug research, discuss the current state and remaining challenges of XL-MS technology, and provide a perspective on the future role XL-MS can play in drug development, with a particular emphasis on PPI modulators.
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Affiliation(s)
- Max Ruwolt
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany. https://twitter.com/@MRuwolt
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany.
| | - Fan Liu
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117 Berlin, Germany.
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3
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Garcia-Del Rio DF, Fournier I, Cardon T, Salzet M. Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry. STAR Protoc 2023; 4:102380. [PMID: 37384523 PMCID: PMC10511867 DOI: 10.1016/j.xpro.2023.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/04/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
Since the start of mass-spectrometry-based proteomics, proteins from non-referenced open reading frames or alternative proteins (AltProts) have been overlooked. Here, we present a protocol to identify human subcellular AltProt and decipher some interactions using cross-linking mass spectrometry. We describe steps for cell culture, in cellulo cross-link, subcellular extraction, and sequential digestion. We then detail both liquid chromatography-tandem mass spectrometry and cross-link data analyses. The implementation of a single workflow allows the non-targeted identification of signaling pathways involving AltProts. For complete details on the use and execution of this protocol, please refer to Garcia-del Rio et al.1.
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Affiliation(s)
- Diego Fernando Garcia-Del Rio
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France; VIB Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
| | - Isabelle Fournier
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Tristan Cardon
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Michel Salzet
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
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4
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Birklbauer MJ, Matzinger M, Müller F, Mechtler K, Dorfer V. MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity. J Proteome Res 2023; 22:3009-3021. [PMID: 37566781 PMCID: PMC10476269 DOI: 10.1021/acs.jproteome.3c00325] [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: 05/31/2023] [Indexed: 08/13/2023]
Abstract
Cross-linking mass spectrometry has become a powerful tool for the identification of protein-protein interactions and for gaining insight into the structures of proteins. We previously published MS Annika, a cross-linking search engine which can accurately identify cross-linked peptides in MS2 spectra from a variety of different MS-cleavable cross-linkers. In this publication, we present MS Annika 2.0, an updated version implementing a new search algorithm that, in addition to MS2 level, only supports the processing of data from MS2-MS3-based approaches for the identification of peptides from MS3 spectra, and introduces a novel scoring function for peptides identified across multiple MS stages. Detected cross-links are validated by estimating the false discovery rate (FDR) using a target-decoy approach. We evaluated the MS3-search-capabilities of MS Annika 2.0 on five different datasets covering a variety of experimental approaches and compared it to XlinkX and MaXLinker, two other cross-linking search engines. We show that MS Annika detects up to 4 times more true unique cross-links while simultaneously yielding less false positive hits and therefore a more accurate FDR estimation than the other two search engines. All mass spectrometry proteomics data along with result files have been deposited to the ProteomeXchange consortium via the PRIDE partner repository with the dataset identifier PXD041955.
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Affiliation(s)
- Micha J. Birklbauer
- Bioinformatics
Research Group, University of Applied Sciences
Upper Austria, Softwarepark
11, 4232 Hagenberg, Austria
| | - Manuel Matzinger
- Research
Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Fränze Müller
- Research
Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Karl Mechtler
- Research
Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
- Institute
of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna
BioCenter (VBC), Dr.
Bohr-Gasse 3, 1030 Vienna, Austria
- Gregor
Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter
(VBC), Dr. Bohr-Gasse
3, 1030 Vienna, Austria
| | - Viktoria Dorfer
- Bioinformatics
Research Group, University of Applied Sciences
Upper Austria, Softwarepark
11, 4232 Hagenberg, Austria
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5
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Ruwolt M, He Y, Borges Lima D, Barshop W, Broichhagen J, Huguet R, Viner R, Liu F. Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity. Anal Chem 2023; 95:5248-5255. [PMID: 36926872 PMCID: PMC10061366 DOI: 10.1021/acs.analchem.2c05141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is a universal tool for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental advances improved cross-link identification by enriching the cross-linker-modified peptides chemically with the use of enrichable cross-linkers. However, mono-links (i.e., peptides modified with a hydrolyzed cross-linker) still hinder efficient cross-link identification since a large proportion of measurement time is spent on their MS2 acquisition. Currently, cross-links and mono-links cannot be separated by sample preparation techniques or chromatography because they are chemically almost identical. Here, we found that based on the intensity ratios of four diagnostic peaks when using PhoX/tBu-PhoX cross-linkers, cross-links and mono-links can be partially distinguished. Harnessing their characteristic intensity ratios for real-time library search (RTLS)-based triggering of high-resolution MS2 scans increased the number of cross-link identifications from both single protein samples and intact E. coli cells. Specifically, RTLS improves cross-link identification from unenriched samples and short gradients, emphasizing its advantages in high-throughput approaches and when instrument time or sample amount is limited.
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Affiliation(s)
- Max Ruwolt
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - Yi He
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Diogo Borges Lima
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - William Barshop
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Johannes Broichhagen
- Department of Chemical Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Fan Liu
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin 13125, Germany.,Charité─Universitätsmedizin Berlin, Charitépl. 1, Berlin 10117, Germany
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6
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Cross-linking mass spectrometry for mapping protein complex topologies in situ. Essays Biochem 2023; 67:215-228. [PMID: 36734207 PMCID: PMC10070479 DOI: 10.1042/ebc20220168] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/04/2023]
Abstract
Cross-linking mass spectrometry has become an established technology to provide structural information on the topology and dynamics of protein complexes. Readily accessible workflows can provide detailed data on simplified systems, such as purified complexes. However, using this technology to study the structure of protein complexes in situ, such as in organelles, cells, and even tissues, is still a technological frontier. The complexity of these systems remains a considerable challenge, but there have been dramatic improvements in sample handling, data acquisition, and data processing. Here, we summarise these developments and describe the paths towards comprehensive and comparative structural interactomes by cross-linking mass spectrometry.
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7
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Zhou C, Dai S, Lin Y, Lian S, Fan X, Li N, Yu W. Exhaustive Cross-Linking Search with Protein Feedback. J Proteome Res 2023; 22:101-113. [PMID: 36480279 DOI: 10.1021/acs.jproteome.2c00500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Improving the sensitivity of protein-protein interaction detection and protein structure probing is a principal challenge in cross-linking mass spectrometry (XL-MS) data analysis. In this paper, we propose an exhaustive cross-linking search method with protein feedback (ECL-PF) for cleavable XL-MS data analysis. ECL-PF adopts an optimized α/β mass detection scheme and establishes protein-peptide association during the identification of cross-linked peptides. Existing major scoring functions can all benefit from the ECL-PF workflow to a great extent. In comparisons using synthetic data sets and hybrid simulated data sets, ECL-PF achieved 3-fold higher sensitivity over standard techniques. In experiments using real data sets, it also identified 65.6% more cross-link spectrum matches and 48.7% more unique cross-links.
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Affiliation(s)
- Chen Zhou
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Shuaijian Dai
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Yuanqiao Lin
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Sheng Lian
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong 999077, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, 518000, China
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, 518000, China
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8
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Matzinger M, Vasiu A, Madalinski M, Müller F, Stanek F, Mechtler K. Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows. Nat Commun 2022; 13:3975. [PMID: 35803948 PMCID: PMC9270371 DOI: 10.1038/s41467-022-31701-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/21/2022] [Indexed: 11/09/2022] Open
Abstract
Cross-linking mass spectrometry has matured to a frequently used tool for the investigation of protein structures as well as interactome studies up to a system-wide level. The growing community generated a broad spectrum of applications, linker types, acquisition strategies and specialized data analysis tools, which makes it challenging to decide for an appropriate analysis workflow. Here, we report a large and flexible synthetic peptide library as reliable instrument to benchmark crosslink workflows. Additionally, we provide a tool, IMP-X-FDR, that calculates the real, experimentally validated, FDR, compares results across search engine platforms and analyses crosslink properties in an automated manner. We apply the library with 6 commonly used linker reagents and analyse the data with 6 established search engines. We thereby show that the correct algorithm and search setting choice is highly important to improve identification rate and reliability. We reach identification rates of up to ~70 % of the theoretical maximum (i.e. 700 unique lysine-lysine cross-links) while maintaining a real false-discovery-rate of <3 % at cross-link level with high reproducibility, representatively showing that our test system delivers valuable and statistically solid results. Cross-linking mass spectrometry is widely used to elucidate protein structures and interactions. Here, the authors generate an extensive peptide library to benchmark the most common cross-link search engines with frequently used cross-linking reagents in low and high complex sample systems.
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Affiliation(s)
- Manuel Matzinger
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| | - Adrian Vasiu
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Mathias Madalinski
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Fränze Müller
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Florian Stanek
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria. .,Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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9
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Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons. Chem Rev 2021; 122:7500-7531. [PMID: 34797068 DOI: 10.1021/acs.chemrev.1c00786] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this review, the contributions of chemical cross-linking combined with mass spectrometry (XL-MS) for studying three-dimensional structures of proteins and for investigating protein-protein interactions are outlined. We summarize the most important cross-linking reagents, software tools, and XL-MS workflows and highlight prominent examples for characterizing proteins, their assemblies, and interaction networks in vitro and in vivo. Computational modeling plays a crucial role in deriving 3D-structural information from XL-MS data. Integrating XL-MS with other techniques of structural biology, such as cryo-electron microscopy, has been successful in addressing biological questions that to date could not be answered. XL-MS is therefore expected to play an increasingly important role in structural biology in the future.
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Affiliation(s)
- Lolita Piersimoni
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Biozentrum, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
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10
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Yugandhar K, Zhao Q, Gupta S, Xiong D, Yu H. Progress in methodologies and quality-control strategies in protein cross-linking mass spectrometry. Proteomics 2021; 21:e2100145. [PMID: 34647422 DOI: 10.1002/pmic.202100145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/04/2021] [Indexed: 11/10/2022]
Abstract
Deciphering the interaction networks and structural dynamics of proteins is pivotal to better understanding their biological functions. Cross-linking mass spectrometry (XL-MS) is a powerful and increasingly popular technology that provides information about protein-protein interactions and their structural constraints for individual proteins and multiprotein complexes on a proteome-scale. In this review, we first assess the coverage and depth of the XL-MS technique by utilizing publicly available datasets. We then delve into the progress in XL-MS experimental and computational methodologies and examine different quality-control strategies reported in the literature. Finally, we discuss the progress in XL-MS applications along with the scope for future improvements.
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Affiliation(s)
- Kumar Yugandhar
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Qiuye Zhao
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Shobhita Gupta
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Dapeng Xiong
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
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11
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Huang R, Zhu W, Xu Z, Chen J, Jiang B, Chen H, Chen W. Accurate Retention Time Prediction Based on Monolinked Peptide Information to Confidently Identify Cross-Linked Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2410-2416. [PMID: 34320809 DOI: 10.1021/jasms.1c00120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cross-linking mass spectrometry methods have not been successfully applied to protein-protein interaction discovery at a proteome-wide level mainly due to the computation complexity (O (n2)) issue. In a previous report, we proposed a decision tree searching strategy (DTSS), which can reduce complexity by orders of magnitude. In this study, we further found that the monolinked peptides carry out the information on the retention time of the corresponding cross-linked pairs; therefore, the retention time of cross-linked peptide pairs can be predicted accurately. By utilizing the retention time as an extra filter, the false positive rate can be reduced by around 86% with a sensitivity loss of 10%. The method combined with DTSS (T-DTSS) not only benefits improving identification confidence but also leads to lower cutoff scores and facilitates substantially increasing inter-cross-link identification. T-DTSS was successfully applied to the identification of inter-cross-links obtained from Escherichia coli cell lysate cross-linked by a newly synthesized enrichable cross-linker, pDSBE. The approach can be applicable to both cleavable and noncleavable methods.
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Affiliation(s)
- Rong Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Zili Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Jiakang Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Hongli Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Wenzhang Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
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12
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Ziemianowicz DS, Saltzberg D, Pells T, Crowder DA, Schräder C, Hepburn M, Sali A, Schriemer DC. IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics. Mol Cell Proteomics 2021; 20:100139. [PMID: 34418567 PMCID: PMC8452774 DOI: 10.1016/j.mcpro.2021.100139] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/27/2021] [Accepted: 08/11/2021] [Indexed: 11/01/2022] Open
Abstract
Proteomics methodology has expanded to include protein structural analysis, primarily through cross-linking mass spectrometry (XL-MS) and hydrogen-deuterium exchange mass spectrometry (HX-MS). However, while the structural proteomics community has effective tools for primary data analysis, there is a need for structure modeling pipelines that are accessible to the proteomics specialist. Integrative structural biology requires the aggregation of multiple distinct types of data to generate models that satisfy all inputs. Here, we describe IMProv, an app in the Mass Spec Studio that combines XL-MS data with other structural data, such as cryo-EM densities and crystallographic structures, for integrative structure modeling on high-performance computing platforms. The resource provides an easily deployed bundle that includes the open-source Integrative Modeling Platform program (IMP) and its dependencies. IMProv also provides functionality to adjust cross-link distance restraints according to the underlying dynamics of cross-linked sites, as characterized by HX-MS. A dynamics-driven conditioning of restraint values can improve structure modeling precision, as illustrated by an integrative structure of the five-membered Polycomb Repressive Complex 2. IMProv is extensible to additional types of data.
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Affiliation(s)
- Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Daniel Saltzberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, California, USA
| | - Troy Pells
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Christoph Schräder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Morgan Hepburn
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, California, USA
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada; Department of Chemistry, University of Calgary, Calgary, Alberta, Canada.
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13
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Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry. Proc Natl Acad Sci U S A 2021; 118:2023360118. [PMID: 34349018 DOI: 10.1073/pnas.2023360118] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Defining protein-protein interactions (PPIs) in their native environment is crucial to understanding protein structure and function. Cross-linking-mass spectrometry (XL-MS) has proven effective in capturing PPIs in living cells; however, the proteome coverage remains limited. Here, we have developed a robust in vivo XL-MS platform to facilitate in-depth PPI mapping by integrating a multifunctional MS-cleavable cross-linker with sample preparation strategies and high-resolution MS. The advancement of click chemistry-based enrichment significantly enhanced the detection of cross-linked peptides for proteome-wide analyses. This platform enabled the identification of 13,904 unique lysine-lysine linkages from in vivo cross-linked HEK 293 cells, permitting construction of the largest in vivo PPI network to date, comprising 6,439 interactions among 2,484 proteins. These results allowed us to generate a highly detailed yet panoramic portrait of human interactomes associated with diverse cellular pathways. The strategy presented here signifies a technological advancement for in vivo PPI mapping at the systems level and can be generalized for charting protein interaction landscapes in any organisms.
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14
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Gutierrez C, Salituro LJ, Yu C, Wang X, DePeter SF, Rychnovsky SD, Huang L. Enabling Photoactivated Cross-Linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-Cleavable Cross-Linkers. Mol Cell Proteomics 2021; 20:100084. [PMID: 33915260 PMCID: PMC8214149 DOI: 10.1016/j.mcpro.2021.100084] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/02/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
Cross-linking mass spectrometry (XL-MS) is a powerful tool for studying protein-protein interactions and elucidating architectures of protein complexes. While residue-specific XL-MS studies have been very successful, accessibility of interaction regions nontargetable by specific chemistries remain difficult. Photochemistry has shown great potential in capturing those regions because of nonspecific reactivity, but low yields and high complexities of photocross-linked products have hindered their identification, limiting current studies predominantly to single proteins. Here, we describe the development of three novel MS-cleavable heterobifunctional cross-linkers, namely SDASO (Succinimidyl diazirine sulfoxide), to enable fast and accurate identification of photocross-linked peptides by MSn. The MSn-based workflow allowed SDASO XL-MS analysis of the yeast 26S proteasome, demonstrating the feasibility of photocross-linking of large protein complexes for the first time. Comparative analyses have revealed that SDASO cross-linking is robust and captures interactions complementary to residue-specific reagents, providing the foundation for future applications of photocross-linking in complex XL-MS studies.
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Affiliation(s)
- Craig Gutierrez
- Department of Physiology and Biophysics, University of California, Irvine, California, USA
| | - Leah J Salituro
- Department of Chemistry, University of California, Irvine, California, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, California, USA
| | - Xiaorong Wang
- Department of Physiology and Biophysics, University of California, Irvine, California, USA
| | - Sadie F DePeter
- Department of Chemistry, University of California, Irvine, California, USA
| | - Scott D Rychnovsky
- Department of Chemistry, University of California, Irvine, California, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, California, USA.
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15
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Kalathiya U, Padariya M, Faktor J, Coyaud E, Alfaro JA, Fahraeus R, Hupp TR, Goodlett DR. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS). Biomolecules 2021; 11:382. [PMID: 33806612 PMCID: PMC8001575 DOI: 10.3390/biom11030382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/28/2022] Open
Abstract
The fundamentals of how protein-protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein-protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.
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Affiliation(s)
- Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Etienne Coyaud
- Protéomique Réponse Inflammatoire Spectrométrie de Mass—PRISM, Inserm U1192, University Lille, CHU Lille, F-59000 Lille, France;
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8Z 7X8, Canada
- Genome BC Proteome Centre, University of Victoria, Victoria, BC V8Z 5N3, Canada
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16
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Matzinger M, Mechtler K. Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction Networks in Vivo. J Proteome Res 2021; 20:78-93. [PMID: 33151691 PMCID: PMC7786381 DOI: 10.1021/acs.jproteome.0c00583] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 12/11/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) has matured into a potent tool to identify protein-protein interactions or to uncover protein structures in living cells, tissues, or organelles. The unique ability to investigate the interplay of proteins within their native environment delivers valuable complementary information to other advanced structural biology techniques. This Review gives a comprehensive overview of the current possible applications as well as the remaining limitations of the technique, focusing on cross-linking in highly complex biological systems like cells, organelles, or tissues. Thanks to the commercial availability of most reagents and advances in user-friendly data analysis, validation, and visualization tools, studies using XL-MS can, in theory, now also be utilized by nonexpert laboratories.
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Affiliation(s)
- Manuel Matzinger
- Research
Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Karl Mechtler
- Research
Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
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17
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Cardon T, Franck J, Coyaud E, Laurent EMN, Damato M, Maffia M, Vergara D, Fournier I, Salzet M. Alternative proteins are functional regulators in cell reprogramming by PKA activation. Nucleic Acids Res 2020; 48:7864-7882. [PMID: 32324228 PMCID: PMC7641301 DOI: 10.1093/nar/gkaa277] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/06/2020] [Accepted: 04/21/2020] [Indexed: 12/28/2022] Open
Abstract
It has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial–mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies.
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Affiliation(s)
- Tristan Cardon
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Julien Franck
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Etienne Coyaud
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Estelle M N Laurent
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Marina Damato
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France.,Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Isabelle Fournier
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France.,Institut Universitaire de France (IUF),75005 Paris, France
| | - Michel Salzet
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France.,Institut Universitaire de France (IUF),75005 Paris, France
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18
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Piersimoni L, Sinz A. Cross-linking/mass spectrometry at the crossroads. Anal Bioanal Chem 2020; 412:5981-5987. [PMID: 32472143 PMCID: PMC7442761 DOI: 10.1007/s00216-020-02700-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/01/2020] [Accepted: 05/08/2020] [Indexed: 01/01/2023]
Abstract
Cross-linking/mass spectrometry (XL-MS) has come a long way. Originally, XL-MS was used to study relatively small, purified proteins. Meanwhile, it is employed to investigate protein-protein interactions on a proteome-wide level, giving snapshots of cellular processes. Currently, XL-MS is at the intersection of a multitude of workflows and the impact this technique has in addressing specific biological questions is steadily growing. This article is intended to give a bird's-eye view of the current status of XL-MS, the benefits of using MS-cleavable cross-linkers, and the challenges posed in the future development of this powerful technology. We also illustrate how XL-MS can deliver valuable structural insights into protein complexes when used in combination with other structural techniques, such as electron microscopy. Graphical abstract.
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Affiliation(s)
- Lolita Piersimoni
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Charles Tanford Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Charles Tanford Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany.
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19
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Yu C, Novitsky EJ, Cheng NW, Rychnovsky SD, Huang L. Exploring Spacer Arm Structures for Designs of Asymmetric Sulfoxide-Containing MS-Cleavable Cross-Linkers. Anal Chem 2020; 92:6026-6033. [PMID: 32202417 PMCID: PMC7363200 DOI: 10.1021/acs.analchem.0c00298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) has become a powerful structural tool for defining protein-protein interactions (PPIs) and elucidating architectures of large protein assemblies. To advance XL-MS studies, we have previously developed a series of sulfoxide-containing MS-cleavable cross-linkers to facilitate the detection and identification of cross-linked peptides using multistage mass spectrometry (MSn). While current sulfoxide-based cross-linkers are effective for in vivo and in vitro XL-MS studies at the systems-level, new reagents are still needed to help expand PPI coverage. To this end, we have designed and synthesized six variable-length derivatives of disuccinimidyl sulfoxide (DSSO) to better understand the effects of spacer arm modulation on MS-cleavability, fragmentation characteristics, and MS identification of cross-linked peptides. In addition, the impact on cross-linking reactivity was evaluated. Moreover, alternative MS2-based workflows were explored to determine their feasibility for analyzing new sulfoxide-containing cross-linked products. Based on the results of synthetic peptides and a model protein, we have further demonstrated the robustness and predictability of sulfoxide chemistry in designing MS-cleavable cross-linkers. Importantly, we have identified a unique asymmetric design that exhibits preferential fragmentation of cross-links over peptide backbones, a desired feature for MSn analysis. This work has established a solid foundation for further development of sulfoxide-containing MS-cleavable cross-linkers with new functionalities.
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Affiliation(s)
- Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Eric J. Novitsky
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Nicholas W. Cheng
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | | | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
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20
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Matzinger M, Kandioller W, Doppler P, Heiss EH, Mechtler K. Fast and Highly Efficient Affinity Enrichment of Azide-A-DSBSO Cross-Linked Peptides. J Proteome Res 2020; 19:2071-2079. [PMID: 32250121 PMCID: PMC7199212 DOI: 10.1021/acs.jproteome.0c00003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Cross-linking mass spectrometry is
an increasingly used, powerful
technique to study protein–protein interactions or to provide
structural information. Due to substochiometric reaction efficiencies,
cross-linked peptides are usually low abundance. This results in challenging
data evaluation and the need for an effective enrichment. Here we
describe an improved, easy to implement, one-step method to enrich
azide-tagged, acid-cleavable disuccinimidyl bis-sulfoxide (DSBSO)
cross-linked peptides using dibenzocyclooctyne (DBCO) coupled Sepharose
beads. We probed this method using recombinant Cas9 and E. coli ribosome. For Cas9, the number of detectable cross-links was increased
from ∼100 before enrichment to 580 cross-links after enrichment.
To mimic a cellular lysate, E. coli ribosome
was spiked into a tryptic HEK background at a ratio of 1:2–1:100.
The number of detectable unique cross-links was maintained high at
∼100. The estimated enrichment efficiency was improved by a
factor of 4–5 (based on XL numbers) compared to enrichment
via biotin and streptavidin. We were still able to detect cross-links
from 0.25 μg cross-linked E. coli ribosomes
in a background of 100 μg tryptic HEK peptides, indicating a
high enrichment sensitivity. In contrast to conventional enrichment
techniques, like SEC, the time needed for preparation and MS measurement
is significantly reduced. This robust, fast, and selective enrichment
method for azide-tagged linkers will contribute to mapping protein–protein
interactions, investigating protein architectures in more depth, and
helping to understand complex biological processes.
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Affiliation(s)
- Manuel Matzinger
- Department of Pharmacognosy, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria.,Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Wolfgang Kandioller
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Philipp Doppler
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, 1040 Vienna, Austria
| | - Elke H Heiss
- Department of Pharmacognosy, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.,Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
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21
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Shurpik DN, Mostovaya OA, Sevastyanov DA, Lenina OA, Sapunova AS, Voloshina AD, Petrov KA, Kovyazina IV, Cragg PJ, Stoikov II. Supramolecular neuromuscular blocker inhibition by a pillar[5]arene through aqueous inclusion of rocuronium bromide. Org Biomol Chem 2019; 17:9951-9959. [PMID: 31729508 DOI: 10.1039/c9ob02215e] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A water-soluble pillar[5]arene, decafunctionalized with thioether and carboxylate fragments, was synthesized as a structural analogue of Sugammadex. Its ability to restore the contraction of the diaphragm muscle by encapsulating the muscle relaxant rocuronium bromide was demonstrated. Using UV-vis, NMR and fluorescence spectroscopy, it was shown that the muscle relaxant is associated with the pillar[5]arene with an association constant of 4500 M-1 and a stoichiometry of 1 : 1. The structure of the inclusion complex of the pillar[5]arene with rocuronium bromide was additionally investigated by quantum chemical methods.
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Affiliation(s)
- Dmitriy N Shurpik
- Kazan Federal University, A.M. Butlerov Chemical Institute, 420008 Kremlevskaya, 18, Kazan, Russian Federation.
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22
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Stadlmeier M, Runtsch LS, Streshnev F, Wühr M, Carell T. A Click-Chemistry-Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry. Chembiochem 2019; 21:103-107. [PMID: 31593346 PMCID: PMC6980279 DOI: 10.1002/cbic.201900611] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Indexed: 11/17/2022]
Abstract
Mass spectrometry is the method of choice for the characterisation of proteomes. Most proteins operate in protein complexes, in which their close association modulates their function. However, with standard MS analysis, information on protein–protein interactions is lost and no structural information is retained. To gain structural and interactome data, new crosslinking reagents are needed that freeze inter‐ and intramolecular interactions. Herein, the development of a new reagent, which has several features that enable highly sensitive crosslinking MS, is reported. The reagent enables enrichment of crosslinked peptides from the majority of background peptides to facilitate efficient detection of low‐abundant crosslinked peptides. Due to the special cleavable properties, the reagent can be used for MS2 and potentially for MS3 experiments. Thus, the new crosslinking reagent, in combination with high‐end MS, should enable sensitive analysis of interactomes, which will help researchers to obtain important insights into cellular states in health and diseases.
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Affiliation(s)
- Michael Stadlmeier
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
- Department of Molecular Biology and theLewis-Sigler Institute for Integrative GenomicsPrinceton UniversityWashington RoadPrincetonNJ08544USA
| | - Leander Simon Runtsch
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Filipp Streshnev
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Martin Wühr
- Department of Molecular Biology and theLewis-Sigler Institute for Integrative GenomicsPrinceton UniversityWashington RoadPrincetonNJ08544USA
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
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23
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Genereux JC. Mass spectrometric approaches for profiling protein folding and stability. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 118:111-144. [PMID: 31928723 DOI: 10.1016/bs.apcsb.2019.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein stability reports on protein homeostasis, function, and binding interactions, such as to other proteins, metabolites and drugs. As such, there is a pressing need for technologies that can report on protein stability. The ideal technique could be applied in vitro or in vivo systems, proteome-wide, independently of matrix, under native conditions, with residue-level resolution, and on protein at endogenous levels. Mass spectrometry has rapidly become a preferred technology for identifying and quantifying proteins. As such, it has been increasingly incorporated into methodologies for interrogating protein stability and folding. Although no single technology can satisfy all desired applications, several emerging approaches have shown outstanding success at providing biological insight into the stability of the proteome. This chapter outlines some of these recent emerging technologies.
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Affiliation(s)
- Joseph C Genereux
- Department of Chemistry, University of California, Riverside, CA, United States
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24
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Stieger CE, Doppler P, Mechtler K. Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents. J Proteome Res 2019; 18:1363-1370. [DOI: 10.1021/acs.jproteome.8b00947] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Christian E. Stieger
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Philipp Doppler
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna 1030, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
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25
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Klykov O, Steigenberger B, Pektaş S, Fasci D, Heck AJR, Scheltema RA. Efficient and robust proteome-wide approaches for cross-linking mass spectrometry. Nat Protoc 2018; 13:2964-2990. [DOI: 10.1038/s41596-018-0074-x] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Hagen SE, Liu K, Jin Y, Piersimoni L, Andrews PC, Showalter HD. Synthesis of CID-cleavable protein crosslinking agents containing quaternary amines for structural mass spectrometry. Org Biomol Chem 2018; 16:8245-8248. [PMID: 29537042 PMCID: PMC6138586 DOI: 10.1039/c8ob00329g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Two novel cyclic quaternary amine crosslinking probes are synthesized for structural mass spectrometry of protein complexes in solution and for analysis of protein interactions in organellar and whole cell extracts. Each exhibits high aqueous solubility, excellent protein crosslinking efficiencies, low collision induced dissociation (CID) energy fragmentation efficiencies, high stoichiometries of reaction, increased charges of crosslinked peptide ions, and maintenance of overall surface charge balance of crosslinked proteins.
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Affiliation(s)
- Susan E Hagen
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
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27
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Gutierrez CB, Block SA, Yu C, Soohoo SM, Huszagh AS, Rychnovsky SD, Huang L. Development of a Novel Sulfoxide-Containing MS-Cleavable Homobifunctional Cysteine-Reactive Cross-Linker for Studying Protein-Protein Interactions. Anal Chem 2018; 90:7600-7607. [PMID: 29792801 PMCID: PMC6037416 DOI: 10.1021/acs.analchem.8b01287] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) has become an emerging technology for defining protein-protein interactions (PPIs) and elucidating architectures of large protein complexes. Up to now, the most widely used cross-linking reagents target lysines. Although such reagents have been successfully applied to map PPIs at the proteome-wide scale, comprehensive PPI profiling would require additional cross-linking chemistries. Cysteine is one of the most reactive amino acids and an attractive target for cross-linking owing to its unique role in protein structures. Although sulfhydryl-reactive cross-linkers are commercially available, their applications in XL-MS studies remain sparse, likely due to the difficulty in identifying cysteine cross-linked peptides. Previously, we developed a new class of sulfoxide-containing MS-cleavable cross-linkers to enable fast and accurate identification of cross-linked peptides using multistage tandem mass spectrometry (MS n). Here, we present the development of a new sulfoxide-containing MS-cleavable homobifunctional cysteine-reactive cross-linker, bismaleimide sulfoxide (BMSO). We demonstrate that BMSO-cross-linked peptides display the same characteristic fragmentation pattern during collision-induced dissociation (CID) as other sulfoxide-containing MS-cleavable cross-linked peptides, thus permitting their simplified analysis and unambiguous identification by MS n. Additionally, we show that BMSO can complement amine- and acidic-residue-reactive reagents for mapping protein-interaction regions. Collectively, this work not only enlarges the toolbox of MS-cleavable cross-linkers with diverse chemistries, but more importantly expands our capacity and capability of studying PPIs in general.
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Affiliation(s)
- Craig B. Gutierrez
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Sarah A. Block
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Stephanie M. Soohoo
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Alexander S. Huszagh
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | | | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
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28
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Yu C, Huang L. Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology. Anal Chem 2018; 90:144-165. [PMID: 29160693 PMCID: PMC6022837 DOI: 10.1021/acs.analchem.7b04431] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
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29
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Hage C, Falvo F, Schäfer M, Sinz A. Novel Concepts of MS-Cleavable Cross-linkers for Improved Peptide Structure Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2022-2038. [PMID: 28653243 DOI: 10.1007/s13361-017-1712-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/03/2017] [Accepted: 05/07/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is gaining increasing importance as an alternative method for studying protein conformation and for deciphering protein interaction networks. This study is part of our ongoing efforts to develop innovative cross-linking principles for a facile and efficient assignment of cross-linked products. We evaluate two homobifunctional, amine-reactive, and MS-cleavable cross-linkers regarding their potential for automated analysis of cross-linked products. We introduce the bromine phenylurea (BrPU) linker that possesses a unique structure yielding a distinctive fragmentation pattern on collisional activation. Moreover, BrPU delivers the characteristic bromine isotope pattern and mass defect for all cross-linker-decorated fragments. We compare the fragmentation behavior of the BrPU linker with that of our previously described MS-cleavable TEMPO-Bz linker (which consists of a 2,2,6,6-tetramethylpiperidine-1-oxy moiety connected to a benzyl group) that was developed to perform free-radical-initiated peptide sequencing. Comparative collisional activation experiments (collision-induced dissociation and higher-energy collision-induced dissociation) with both cross-linkers were conducted in negative electrospray ionization mode with an Orbitrap Fusion mass spectrometer using five model peptides. As hypothesized in a previous study, the presence of a cross-linked N-terminal aspartic acid residue seems to be the prerequisite for the loss of an intact peptide from the cross-linked products. As the BrPU linker combines a characteristic mass shift with an isotope signature, it presents a more favorable combination for automated assignment of cross-linked products compared with the TEMPO-Bz linker. ᅟ.
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Affiliation(s)
- Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Francesco Falvo
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
- Eurofins Umwelt West GmbH, Vorgebirgsstr. 20, 50389, Wesseling, Germany
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany.
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30
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Iacobucci C, Hage C, Schäfer M, Sinz A. A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2039-2053. [PMID: 28717933 DOI: 10.1007/s13361-017-1744-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies. Graphical Abstract ᅟ.
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Affiliation(s)
- Claudio Iacobucci
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
| | - Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstr. 4, D-50939, Kӧln, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
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31
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Kolbowski L, Mendes ML, Rappsilber J. Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer. Anal Chem 2017; 89:5311-5318. [PMID: 28402676 PMCID: PMC5436099 DOI: 10.1021/acs.analchem.6b04935] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We compared the five different ways of fragmentation available on a tribrid mass spectrometer and optimized their collision energies with regard to optimal sequence coverage of cross-linked peptides. We created a library of bis(sulfosuccinimidyl)suberate (BS3/DSS) cross-linked precursors, derived from the tryptic digests of three model proteins (Human Serum Albumin, creatine kinase, and myoglobin). This enabled in-depth targeted analysis of the fragmentation behavior of 1065 cross-linked precursors using the five fragmentation techniques: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), and the combinations ETciD and EThcD. EThcD gave the best sequence coverage for cross-linked m/z species with high charge density, while HCD was optimal for all others. We tested the resulting data-dependent decision tree against collision energy-optimized single methods on two samples of differing complexity (a mix of eight proteins and a highly complex ribosomal cellular fraction). For the high complexity sample the decision tree gave the highest number of identified cross-linked peptide pairs passing a 5% false discovery rate (on average ∼21% more than the second best, HCD). For the medium complexity sample, the higher speed of HCD proved decisive. Currently, acquisition speed plays an important role in allowing the detection of cross-linked peptides against the background of linear peptides. Enrichment of cross-linked peptides will reduce this role and favor methods that provide spectra of higher quality. Data are available via ProteomeXchange with identifier PXD006131.
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Affiliation(s)
- Lars Kolbowski
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin , 13355 Berlin, Germany
| | - Marta L Mendes
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin , 13355 Berlin, Germany
| | - Juri Rappsilber
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin , 13355 Berlin, Germany.,Wellcome Trust Centre for Cell Biology, University of Edinburgh , Edinburgh EH9 3BF, United Kingdom
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32
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Hage C, Ihling CH, Götze M, Schäfer M, Sinz A. Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:56-68. [PMID: 27418170 DOI: 10.1007/s13361-016-1426-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/14/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS3 experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids. Graphical Abstract ᅟ.
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Affiliation(s)
- Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany
| | - Christian H Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany
| | - Michael Götze
- Institute of Biochemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle, Saale, Germany
| | - Mathias Schäfer
- Department of Chemistry, University Cologne, Greinstr. 4, D-50939, Köln, Germany.
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany.
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33
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Yılmaz Ş, Drepper F, Hulstaert N, Černič M, Gevaert K, Economou A, Warscheid B, Martens L, Vandermarliere E. Xilmass: A New Approach toward the Identification of Cross-Linked Peptides. Anal Chem 2016; 88:9949-9957. [PMID: 27642655 DOI: 10.1021/acs.analchem.6b01585] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient ones. Moreover, cross-linking complements several structural determination approaches such as cryo-EM. Although several computational approaches are available for the annotation of spectra obtained from cross-linked peptides, there remains room for improvement. Here, we present Xilmass, a novel algorithm to identify cross-linked peptides that introduces two new concepts: (i) the cross-linked peptides are represented in the search database such that the cross-linking sites are explicitly encoded, and (ii) the scoring function derived from the Andromeda algorithm was adapted to score against a theoretical tandem mass spectrometry (MS/MS) spectrum that contains the peaks from all possible fragment ions of a cross-linked peptide pair. The performance of Xilmass was evaluated against the recently published Kojak and the popular pLink algorithms on a calmodulin-plectin complex data set, as well as three additional, published data sets. The results show that Xilmass typically had the highest number of identified distinct cross-linked sites and also the highest number of predicted cross-linked sites.
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Affiliation(s)
- Şule Yılmaz
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University , 9000 Ghent, Belgium
| | - Friedel Drepper
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg , 79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg , 79104 Freiburg, Germany
| | - Niels Hulstaert
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University , 9000 Ghent, Belgium
| | - Maša Černič
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins , Jamova Cesta 39, 1000 Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana , 1000 Ljubljana, Slovenia
| | - Kris Gevaert
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium
| | - Anastassios Economou
- KU Leuven-University of Leuven , Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.,Institute of Molecular Biology and Biotechnology-FoRTH and Department of Biology, University of Crete , Iraklio, 71100 Crete, Greece
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg , 79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg , 79104 Freiburg, Germany
| | - Lennart Martens
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University , 9000 Ghent, Belgium
| | - Elien Vandermarliere
- Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University , 9000 Ghent, Belgium
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34
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Leitner A, Faini M, Stengel F, Aebersold R. Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines. Trends Biochem Sci 2016; 41:20-32. [DOI: 10.1016/j.tibs.2015.10.008] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/18/2015] [Accepted: 10/29/2015] [Indexed: 01/30/2023]
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