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Mehta A, Kamal AHM, Cornelius S, Chowdhury SM. Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking Mass Spectrometry (AP-XL-MS) based Proteomics. Methods Mol Biol 2023; 2690:255-267. [PMID: 37450153 DOI: 10.1007/978-1-0716-3327-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Protein-protein interactions (PPIs) are the physical interactions formed among proteins. These interactions are primarily functional, i.e., they arise from specific biomolecular events, and each interaction interface serves a specific purpose. A significant number of methods have been developed for protein interactions in the field of proteomics in the last decade. Advanced mass spectrometry technology significantly contributed to the development of these methods. The rapid advancement of groundbreaking MS technology has greatly aided the mapping of protein interaction from large-data sets comprehensively. This chapter describes the affinity purification (AP) mass spectrometry (MS)-based methods combined with chemical cross-linking (XL) of protein complexes. This chapter includes sample preparation methods involving cell culture, cell treatments with ligands, drugs, and cross-linkers, protein extractions, affinity purification, sodium dodecyl sulfate (SDS) polyacrylamide gel separation, in-solution or in-gel digestion, liquid-chromatography, and mass spectrometry analysis of samples (LC-MS/MS). Application of a cleavable cross-linker, dual cleavable cross-linking technology (DUCCT) in combination with the affinity purification (AP) method has also been described. Methods for data analysis using unmodified and cross-linked peptide analysis are discussed.
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Affiliation(s)
- Ashima Mehta
- Department of Chemistry and Biochemistry, University of Texas, Arlington, TX, USA
| | - Abu Hena Mostafa Kamal
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sharel Cornelius
- Department of Chemistry and Biochemistry, University of Texas, Arlington, TX, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas, Arlington, TX, USA.
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Fang Z, Wanigasekara MSK, Yepremyan A, Lam B, Thapa P, Foss FW, Chowdhury SM. Mass Spectrometry-Cleavable Protein N-Terminal Tagging Strategy for System-Level Protease Activity Profiling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:189-197. [PMID: 34928623 DOI: 10.1021/jasms.1c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Proteolysis is one of the most important protein post-translational modifications (PTMs) that influences the functions, activities, and structures of nearly all proteins during their lifetime. To facilitate the targeted identification of low-abundant proteolytic products, we devised a strategy incorporating a novel biotinylated reagent PFP (pentafluorophenyl)-Rink-biotin to specifically target, enrich and identify proteolytic N-termini. Within the PFP-Rink-biotin reagent, a mass spectrometry (MS)-cleavable feature was designed to assist in the unambiguous confirmation of the enriched proteolytic N-termini. The proof-of-concept study was performed with multiple standard proteins whose N-termini were successfully modified, enriched and identified by a signature ion (SI) in the MS/MS fragmentation, along with the determination of N-terminal peptide sequences by multistage tandem MS of the complementary fragment generated after the cleavage of MS-cleavable bond. For large-scale application, the enrichment and identification of protein N-termini from Escherichia coli cells were demonstrated, facilitated by an in-house developed NTermFinder bioinformatics workflow. We believe this approach will be beneficial in improving the confidence of identifying proteolytic substrates in a native cellular environment.
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Affiliation(s)
- Zixiang Fang
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Maheshika S K Wanigasekara
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Akop Yepremyan
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Brandon Lam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Pawan Thapa
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Frank W Foss
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
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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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New insights into the mechanisms of age-related protein-protein crosslinking in the human lens. Exp Eye Res 2021; 209:108679. [PMID: 34147508 DOI: 10.1016/j.exer.2021.108679] [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: 03/18/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/31/2022]
Abstract
Although protein crosslinking is often linked with aging as well as some age-related diseases, very few molecular details are available on the nature of the amino acids involved, or mechanisms that are responsible for crosslinking. Recent research has shown that several amino acids are able to generate reactive intermediates that ultimately lead to covalent crosslinking through multiple non-enzymatic mechanisms. This information has been derived from proteomic investigations on aged human lenses and the mechanisms of crosslinking, in each case, have been elucidated using model peptides. Residues involved in spontaneous protein-protein crosslinking include aspartic acid, asparagine, cysteine, lysine, phosphoserine, phosphothreonine, glutamic acid and glutamine. It has become clear, therefore, that several amino acids can act as potential sites for crosslinking in the long-lived proteins that are present in aged individuals. Moreover, the lens has been an invaluable model tissue and source of crosslinked proteins from which to determine crosslinking mechanisms that may lead to crosslinking in other human tissues.
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Zacharias AO, Fang Z, Rahman A, Talukder A, Cornelius S, Chowdhury SM. Affinity and chemical enrichment strategies for mapping low‐abundance protein modifications and protein‐interaction networks. J Sep Sci 2020; 44:310-322. [DOI: 10.1002/jssc.202000930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Adway O. Zacharias
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Zixiang Fang
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Aurchie Rahman
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Akash Talukder
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Sharel Cornelius
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Saiful M. Chowdhury
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
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Schnirch L, Nadler-Holly M, Siao SW, Frese CK, Viner R, Liu F. Expanding the Depth and Sensitivity of Cross-Link Identification by Differential Ion Mobility Using High-Field Asymmetric Waveform Ion Mobility Spectrometry. Anal Chem 2020; 92:10495-10503. [PMID: 32643919 DOI: 10.1021/acs.analchem.0c01273] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In cross-linking mass spectrometry (XL-MS), the depth and sensitivity of cross-link detection is often limited by the low abundance of cross-links compared to non-cross-linked peptides in the digestion mixture. To improve the identification efficiency of cross-links, here, we present a gas-phase separation strategy using high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to the Orbitrap Tribrid mass spectrometers. By enabling an additional peptide separation step in the gas phase using the FAIMS device, we increase the number of cross-link identifications by 22% for a medium complex sample and 59% for strong cation exchange-fractionated HEK293T cell lysate in XL-MS experiments using disuccinimidyl sulfoxide (DSSO) cross-linker. When disuccinimidyl suberate (DSS) cross-linker is in use, we are able to boost cross-link identification by 89% for the medium and 100% for the high complex sample compared to the analyses without FAIMS. Furthermore, we show that, for medium complex samples, FAIMS enables the collection of single-shot XL-MS data with a comparable depth to the corresponding sample fractionated by chromatography-based approaches. Altogether, we demonstrate FAIMS is highly beneficial for XL-MS studies by expanding the proteome coverage of cross-links while improving the efficiency and confidence of cross-link identification.
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Affiliation(s)
- Lennart Schnirch
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
| | - Michal Nadler-Holly
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
| | - Siang-Wun Siao
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany.,Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian K Frese
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117 Berlin, Germany
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Pkwy., San Jose, California 95134, United States
| | - Fan Liu
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
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Zhao B, Reilly CP, Davis C, Matouschek A, Reilly JP. Use of Multiple Ion Fragmentation Methods to Identify Protein Cross-Links and Facilitate Comparison of Data Interpretation Algorithms. J Proteome Res 2020; 19:2758-2771. [PMID: 32496805 DOI: 10.1021/acs.jproteome.0c00111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Multiple ion fragmentation methods involving collision-induced dissociation (CID), higher-energy collisional dissociation (HCD) with regular and very high energy settings, and electron-transfer dissociation with supplementary HCD (EThcD) are implemented to improve the confidence of cross-link identifications. Three different S. cerevisiae proteasome samples cross-linked by diethyl suberthioimidate (DEST) or bis(sulfosuccinimidyl)suberate (BS3) are analyzed. Two approaches are introduced to combine interpretations from the above four methods. Working with cleavable cross-linkers such as DEST, the first approach searches for cross-link diagnostic ions and consistency among the best interpretations derived from all four MS2 spectra associated with each precursor ion. Better agreement leads to a more definitive identification. Compatible with both cleavable and noncleavable cross-linkers such as BS3, the second approach multiplies scoring metrics from a number of fragmentation experiments to derive an overall best match. This significantly increases the scoring gap between the target and decoy matches. The validity of cross-links fragmented by HCD alone and identified by Kojak, MeroX, pLink, and Xi was evaluated using multiple fragmentation data. Possible ways to improve the identification credibility are discussed. Data are available via ProteomeXchange with identifier PXD018310.
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Affiliation(s)
- Bingqing Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Colin P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Caroline Davis
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Chakrabarty JK, Bugarin A, Chowdhury SM. Evaluating the performance of an ETD-cleavable cross-linking strategy for elucidating protein structures. J Proteomics 2020; 225:103846. [PMID: 32480079 DOI: 10.1016/j.jprot.2020.103846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/20/2020] [Accepted: 05/24/2020] [Indexed: 01/08/2023]
Abstract
Chemical cross-linking is a powerful strategy for elucidating the structures of protein or protein complexes. The distance constraints obtained from cross-linked peptides represent the three-dimensional structures of the protein complexes. Unfortunately, structural analysis using cross-linking approach demands a significant amount of data to elucidate protein structures. This requires the development of several cleavable cross-linkers with different range of spacer chains. An Electron Transfer Dissociation (ETD) tandem mass spectrometry cleavable bond hydrazone was reported. Its fragmentation with conjugated peptides showed promise for the development of a new ETD cleavable cross-linker. However, no cross-linker was developed utilizing this ETD cleavable bond. For the first time, we attempted to develop an ETD cleavable cross-linker utilizing a hydrazone bond. We overcome the pitfall for the synthesis of this cross-linker and an easy synthesis scheme is reported. In this report, we evaluated the performance of this cross-linker called Hydrazone Incorporated ETD cleavable cross-linker (HI-ETD-XL) in model peptides and proteins. The characteristic fragmentation behavior of HI-ETD-XL during electron transfer dissociation and subsequent sequence identification of the peptide fragment ions by tandem mass spectrometry allowed the identification of cross-linked peptides unambiguously. We believe the availability of this ETD cleavable cross-linker will advance structural proteomics research significantly. SIGNIFICANCE: Many cellular processes rely on the structural dynamics of protein complexes. The detailed knowledge of the structure and dynamics of protein complexes is crucial for understanding their biological functions and regulations. However, most of the structure of these multiprotein entities remain uncharacterized and sometimes is very challenging to reveal with biophysical techniques alone. Chemical cross-linking combined with mass spectrometry (MS) has proven to be a dependable strategy in structural proteomics field. However, data complexity and false identifications are significant hindrances for unambiguous identification of cross-linked peptides. Confident identifications demand structural studies with cross-linkers with different properties and variable spacer chain lengths. This new ETD cleavable cross-linking workflow will provide additional confidence to overcome these drawbacks and allow us to pinpoint cross-linked peptides confidently.
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Affiliation(s)
| | - Alejandro Bugarin
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, USA; Department of Chemistry & Physics, Florida Gulf Coast University, FL, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, USA.
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