Cross-linked peptide characterization software tools | Mass spectrometry-based untargeted proteomics
Mass spectrometry (MS) has increasingly been applied to identify the residues that are involved in chemical cross-links in compound protein assemblies, and have provided valuable insight into the molecular arrangement, orientation and contact surfaces of subunits within such large complexes. This approach is known as MS3D, and involves the MS analysis of cross-linked di-peptides following the enzymatic cleavage of a chemically cross-linked complex.
Searches for cross-linked peptides from complex samples. xQuest searches ion mass spectra (MS2) from isotopically labeled cross-links to identify cross-linked peptides from large protein databases. The key feature of the search engine is a combination of a low stringency search for candidate peptides followed by stringent spectrum matching. The software is able to identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search.
Enables cross-link identification against a complete human proteome database. XlinkX is a cross-link search engine that was built for analyzing a multipronged data set. The software can identify (1) disulfide-bridged peptides and (2) cross-links obtained with non-cleavable cross-linkers, electron-transfer dissociation (ETD) cleavable cross-linkers and collision-induced dissociation (CID). It was applied in a cross-linking study on a full HeLa cell lysate using the mass spectrometry (MS)-cleavable cross-linker.
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.
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.
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.
Analyses protein or peptide sequences. GPMAW lets users to import protein sequences via a built-in web interface to proteolytic digests. It can fragment theoretical peptide, map mass spectrometric peptide and perform query in database. Quick comparison of two related proteins is possible but this tool is not fitting for more than two. It provides the monoisotopic or average protonated mass of the sequence for every sequence window.
Assists users to identify cross linked peptide. MS-Bridge works on several functions such as peptide combination, or link search type. It is possible for users to enter their own protein sequence. Several filters are available and can accelerate the research about cross linked peptide. This tool depends of the ProteinProspector web package.
Evaluates the quality of crosslinked models based on the distances estimated by the Jwalk tool. MNXL scores and validates models via crosslink restraints. This software is only applicable to lysine crosslinkers that are 11.4 Å long because of the dependence of the number of violations and expected solvent accessible surface distance (SASD) to the crosslinker length.
A software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). SIM-XL introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. SIM-XL is the first tool to support XL data in the mzIdentML format.
Automates the detection of cross-links derived from three different tandem mass spectrometry (MS/MS) cleavable cross-linkers. MeroX allows decoy search, by inverting the sequences of the proteins analyzed and performing an identical analysis on the decoy protein sequences. It provides three main functions: (1) recognition of cross-link candidates, (2) scoring of candidates, and (3) a graphical user interface (GUI) for analysis.
Identifies both peptides from a single cross-linked product spectrum but independently assessing the reliability of the least confident peptide identification for setting an acceptance threshold. ProteinProspector contains several tools to mine sequence databases such as MS-Bridge which matches to peptides with a large mass modification when queried. Some functions require a user registration.
Interprets the tandem mass spectra of crosslinked peptides. Popitam is an algorithm designed to associate amino acid sequence with tandem mass spectra of chemically modified peptides. It extracts all sequence tags, according to a user-specified minimum length, that are consistent with the candidate sequence and the m/z pattern of the spectrum. It is able to detect any biological post-translational modifications (PTM), chemical artifact, or, unknown crosslinked peptides.
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.
Interfaces Mascot with Percolator. Mascot Percolator is an extension that works in 3 steps: (i) reads the Mascot results files, (ii) computes the scoring features and uses these for the Percolator training, and (iii) merges the result file of Percolator and the input files to comprise peptide, protein and scoring information. It can be readily integrated into existing pipelines or be used as a stand-alone application.
Conducts exhaustive search for candidates in cross-linked peptides identification. ECL is designed to identify peptides linked by non-cleavable amine-reactive cross linkers. It is robust to noise peaks and can determine the e-value for each peptide-spectrum match (PSM). This tool achieves a linear time and space complexity by taking advantage of the additive property of a score function.
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.
Automates the search for crosslinks formed by site-specifically incorporated crosslinking amino acids in liquid chromatography coupled with tandem mass spectrometry (LC-MS-MS) data. Crossfinder’s scope is to map protein crosslinks formed between site-specifically incorporated crosslinking moieties and other, unknown amino acids in the same or a separate protein with amino acid resolution. It allows re-filtering the data after the analysis.
Integrates cross-linked site information with protein contact maps. XLmap evaluates the overlap between the cross-linking information with the protein contact map over a specified distance range resulting in a CM score. XLmap provides a tool to utilize experimentally derived cross-linking information in protein structural analysis.
Identifies cross-linked peptides with maximum paired scores in a protein sequence database. Xolik is a linear-time algorithm that searches cross-linked peptides in linear time using the data structure of double-ended queue. The software achieves linear time complexity with respect to the number of candidate peptides in the database using the double-ended queue to store the order of scores compared in previous iterations.