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.
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.
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.
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.
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.
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.
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.