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xTract
Encompasses a suite of algorithms that allows the automated processing and statistical validation of quantitative data from quantitative chemical cross-linking-mass spectrometry (qCX-MS) experiments. xTract is a generic and versatile computational framework supporting qCX-MS measurements derived from both stable-isotope-based and label-free quantification (LFQ) strategies. This method is compatible with different experimental designs so that no particular type of isotope-labeled reagent is required.
XL-MOD
An automated modeling method dedicated to large protein assemblies that (i) uses a form of spatial restraints that realistically reflects the distribution of experimentally observed crosslinked distances; (ii) automatically deals with ambiguous and/or conflicting crosslinks and identifies alternative conformations within a Bayesian framework; and (iii) allows subunit structures to be flexible during conformational sampling. XL-MOD addresses major challenges in modeling large protein complexes from crosslinking data as conformational heterogeneity, false positive crosslinks, crosslinks to flexible regions without structural information and errors in the starting structures of the components.
Xlink Analyzer
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A software tool for visualization and analysis of cross-linking mass spectrometry (XL-MS) data in the context of the three-dimensional structures. Xlink Analyzer enables automatic visualization of cross-links, identifies cross-links violating spatial restraints, calculates violation statistics, maps chemically modified surfaces, and allows interactive manipulations that facilitate analysis of XL-MS data and aid designing new experiments.
xVis
Displays crosslinks in clear schematic representations in form of a circular, bar or network diagram. The interactive graphs indicate the linkage sites and identification scores, depict the spatial proximity of structurally and functionally annotated protein regions and the evolutionary conservation of amino acids and facilitate clustering of proteins into subcomplexes according to the crosslink density. Furthermore, xVis offers two options for the qualitative assessment of the crosslink identifications by filtering crosslinks according to identification scores or false discovery rates and by displaying the corresponding fragment ion spectrum of each crosslink for the manual validation of the mass spectrometric data. xVis provides an easy-to-use tool for the fast topological and functional interpretation of distance information on protein complex architectures and for the evaluation of crosslink fragment ion spectra.
ECL
Can exhaustively search all candidates in cross-linked peptides identification. ECL is designed to identify peptides linked by noncleavable amine-reactive cross linkers like DSS and BS3. The experiments showed that ECL could identify more peptides than xQuest, pLink, and ProteinProspector. A further analysis indicated that some of the additional identified results were thanks to the exhaustive search. Finally ECL identified more non-redundant peptides than ProteinProspector and Kojak.
Xwalk
Displays and computes chemical cross-linking of proteins or protein complexes. Xwalk is a Java package that uses grids and a search algorithm to compute the length of the shortest path. It checks that the cross-linked amino acids and the entire solvent accessible surface distance (SASD) path is solvent accessible. Furthermore, Xwalk takes the dynamic disorder of protein segments within X-ray structures into account. This method is available as a command line version or a web app.
CLMSVault
Provides important functionalities for analysis of cross-linked peptides. CLMSVault permits to (i) aggregate cross-link identifications from different cross-linkers and/or search algorithms to provide additional restraints for protein complex models, (ii) provide a label-free quantification workflow for cross-linked peptides across each supported search algorithms, (iii) allow the visualization of cross-link abundance between experimental conditions and (iv) support data dissemination of interaction data in the open PSI-MI TAB and XML file formats.
VIRTUALMSLAB
Allows users to perform a variety of advanced virtual proteomics experiments with mass spectrometry (MS) analyses. VIRTUALMSLAB is a program able to calculate results of: (1) any virtual, complete or partial, protein modification reaction including cleavages, either simultaneously or in any desired order; and (2) in and out filtering of defined reaction products. It aims to furnish procedures for the analysis of naturally occurring cross-links, e.g. disulfide bonds, and artificially introduced cross-links in proteins.
StavroX
A software which has been specifically designed for analyzing highly complex crosslinking datasets. StavroX was evaluated for three diverse biological systems: (1) the complex between calmodulin and a peptide derived from Munc13, (2) an N-terminal ß-laminin fragment, and (3) the complex between guanylyl cyclase activating protein-2 and a peptide derived from retinal guanylyl cyclase. StavroX is expected to give a further push to the chemical crosslinking approach as a routine technique for protein interaction studies.
ICC-CLASS / Isotopically-Coded Cleavable Cross-Linking Analysis Software Suite
Analyses mass spectrometric data obtained with isotopically-coded cleavable crosslinkers. ICC-CLASS contains three programs called: DX, DXDX, and DXMSMS. DX searches the mass spectra for the presence of ion signal doublets resulting from the light and heavy isotopic forms of the isotopically-coded crosslinking reagent used. DXDX searches for possible mass matches between cleaved and uncleaved isotopically-coded crosslinks based on the established chemistry of the cleavage reaction for a given crosslinking reagent. DXMSMS assigns the crosslinks to the known protein sequences, based on the isotopically-coded and un-coded MS/MS fragmentation data of uncleaved and cleaved peptide crosslinks.
xiNET
A visualization tool for exploring cross-linking/mass spectrometry results. The interactive maps of the cross-link network that it generates are a type of node-link diagram. In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures.
MXDB
Identifies cross-linked peptides from mass spectrometry (MS)/MS spectra. MXDB is a database search method that uses a mixture fragmentation model to explicitly account for the co-fragmentation of two peptides. The software also allows a two-stage search strategy, in which it first identifies only one peptide and then identifies the other peptide in the linked pair. It was applied to the identification of chemically crosslinked peptides on two MS/MS datasets: one from the Schizosaccharomyces pombe 26S proteasome complex, and another from the rabbit 20S proteasome complex.
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