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XLinkProphet ReACT XL-MS - Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks

ABSTRACT: Control Data Crosslink ReACT Results Searched with Comet

INSTRUMENT(S): LTQ FT

ORGANISM(S): Equus Caballus (horse) Bos Taurus (bovine) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Andrew Keller

LAB HEAD: James Bruce

PROVIDER: PXD009001 | Pride | 2019-07-12

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	102617_ADH_BDP_mango_2hr_1.mzXML	Mzxml
	102617_ADH_BDP_mango_2hr_1.pep.xml	Pepxml
	102617_alpha_casein_BDP_mango_2hr_1.mzXML	Mzxml
	102617_alpha_casein_BDP_mango_2hr_1.pep.xml	Pepxml
	102617_alpha_lactalbumin_BDP_mango_2hr_1.mzXML	Mzxml

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Publications

Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks.

Keller Andrew A Chavez Juan D JD Bruce James E JE

Bioinformatics (Oxford, England) 20190301 5

<h4>Motivation</h4>Peptides crosslinked with cleavable chemical crosslinkers are identified with mass spectrometry by independent database search of spectra associated with the two linked peptides. A major challenge is to combine together the evidence of the two peptides into an overall assessment of the two-peptide crosslink.<h4>Results</h4>Here, we describe software that models crosslink specific information to automatically validate XL-MS cleavable peptide crosslinks. Using a dataset of cross ...[more]

PMID: 30137231

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Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks.

Project description:MOTIVATION:Peptides crosslinked with cleavable chemical crosslinkers are identified with mass spectrometry by independent database search of spectra associated with the two linked peptides. A major challenge is to combine together the evidence of the two peptides into an overall assessment of the two-peptide crosslink. RESULTS:Here, we describe software that models crosslink specific information to automatically validate XL-MS cleavable peptide crosslinks. Using a dataset of crosslinked protein mixtures, we demonstrate that it computes accurate and highly discriminating probabilities, enabling as many as 75% more identifications than was previously possible using only search scores and a predictable false discovery rate. AVAILABILITY AND IMPLEMENTATION:XLinkProphet software is freely available on the web at http://brucelab.gs.washington.edu. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

| S-EPMC6394394 | biostudies-literature

Mango-EcoliBDP - Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification

Project description:Dataset presented in Mango manuscript. Contains Ecoli cross-linked with BDP-NHP. Demonstration of whole proteome in-vivo cross-linking without an instrument capable of serial fragmentation.

2019-02-25 | PXD008975 | Pride

Novel roles for ribosomal histidine methylation revealed by proteomics and large-scale cross-linking mass spectrometry

Project description:The methylation of histidine residues is increasingly found to be both prevalent throughout the proteome, and also relevant to human disease. Hpm1p mono-methylates H243 in the ribosomal protein Rpl3 and represents the only histidine methyltransferase in Saccharomyces cerevisiae. Interestingly, the hpm1 deletion strain is highly pleiotropic, with many extra-ribosomal phenotypes including improved growth rates in alternative carbon sources. Here we aimed to understand how methylation of one histidine in one ribosomal protein could result in such diverse phenotypes by combining targeted mass spectrometry, growth assays, quantitative proteomics and cross-linking mass spectrometry. We confirmed the localisation and stoichiometry of the H243 site, found unreported sensitivities of Δhpm1 yeast to non-ribosomal stressors, and identified thirty differentially-abundant proteins upon hpm1 knockout, most with clear links to the coordination of sugar metabolism. We adapted the emerging technique of quantitative large scale cross-linking mass spectrometry for use in budding yeast, which resulted in the identification of 1,267 unique in vivo lysine-lysine pairs. By reproducibly monitoring over 350, we detected changes to membrane protein structure, chromatin compaction, and mitochondrial protein-protein interactions, independently of changes in protein abundance themselves. Taken together, these studies reveal a clear role for Hpm1p in the coordination of sugar metabolism, contextualise the deletion strain’s pleiotropy and illustrate how cross-linking mass spectrometry can generate mechanistic insights into complex cellular processes.

2022-08-12 | PXD027953 | Pride

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HeLa Cells Cross-Linked In Vivo versus as a Lysate

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Identification of MS-Cleavable and Non-Cleavable Chemically Crosslinked Peptides with MetaMorpheus

Project description:The present work describes a novel search program for the detection of both MS-cleavable and non-cleavable crosslinked peptides and it is the first software program reported with both capacities. The search strategy has been implemented in the computer program MetaMorpheus, which has a user-friendly graphical user interface (GUI). Novel crosslinker molecules can be easily added if desired. A fragment-ion index scheme makes the search computationally efficient. DSSO crosslinked BSA and E.coli ribosome data were used to validate the MS-cleavable crosslink search results.

2018-07-16 | PXD009000 | Pride

A High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid

Project description:In conventional crosslinking mass spectrometry, proteins are crosslinked using a highly selective, bifunctional chemical reagent, which limits crosslinks to residues that are accessible and reactive to the reagent. Genetically incorporating a photoreactive amino acid offers two key advantages: any site can be targeted, including those that are inaccessible to conventional crosslinking reagents, and photoreactive amino acids can potentially react with a broad range of interaction partners. However, broad reactivity imposes additional challenges for crosslink identification. In this study, we incorporate benzoylphenylalanine (BPA), a photoreactive amino acid, at selected sites in an intrinsically disordered region of the human protein HSPB5. We report and characterize a workflow for identifying and visualizing residue-level interactions originating from BPA. We routinely identify 30 to 300 crosslinked peptide spectral matches with this workflow, which is up to ten times more than existing tools for residue-level BPA crosslink identification. Most identified crosslinks are assigned to a precision of one or two residues, which is supported by a high degree of overlap between replicate analyses. Based on these results, we anticipate that this workflow will support the more general use of genetically incorporated, photoreactive amino acids for characterizing the structures of proteins that have resisted high-resolution characterization.

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