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Cross-linked peptide identification software tools | MS-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…
Xlink Analyzer
Desktop

Xlink Analyzer

A software tool for visualization and analysis of cross-linking mass…

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…

xTract
Desktop

xTract

Encompasses a suite of algorithms that allows the automated processing and…

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.…

xQuest
Desktop
Web

xQuest

Searches for cross-linked peptides from complex samples. xQuest searches ion…

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.…

pLink
Desktop

pLink

Software dedicated for the analysis of chemically cross-linked proteins or…

Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.

XL-MOD
Desktop

XL-MOD

An automated modeling method dedicated to large protein assemblies that (i)…

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…

pLink-SS
Desktop

pLink-SS

Helps users by providing accurate identification of disulfide-linked peptides.…

Helps users by providing accurate identification of disulfide-linked peptides. pLink-SS is a high-throughput mass spectrometry (MS) method that performs disulfide proteome analyses and identified…

Xwalk
Web
Desktop

Xwalk

Displays and computes chemical cross-linking of proteins or protein complexes.…

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…

XLinkDB
Dataset

XLinkDB

Serves as a data storage site and visualization tool for cross-linking results.…

Serves as a data storage site and visualization tool for cross-linking results. XLink-DB accepts data generated with any cross-linker and stores them in a relational database. Cross-linked sites are…

xVis
Desktop
Web

xVis

Displays crosslinks in clear schematic representations in form of a circular,…

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…

MXDB
Desktop

MXDB

Identifies cross-linked peptides from mass spectrometry (MS)/MS spectra. 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…

ECL
Desktop

ECL

Can exhaustively search all candidates in cross-linked peptides identification.…

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…

ProXL
Dataset

ProXL Protein Cross-linking Database

A web application accompanying database designed for sharing, visualizing, and…

A web application accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality…

Hekate
Desktop

Hekate

A suite of tools that address the challenges involved in analysing protein…

A suite of tools that address the challenges involved in analysing protein cross-linking experiments when combined with mass spectrometry.

CLMSVault
Web
Desktop

CLMSVault

Provides important functionalities for analysis of cross-linked peptides.…

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…

xiNET
Web

xiNET

A visualization tool for exploring cross-linking/mass spectrometry results. The…

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…

Crossfinder
Desktop

Crossfinder

Protein crosslinking has been used for decades to derive structural information…

Protein crosslinking has been used for decades to derive structural information about proteins and protein complexes. Crossfinder automates the search for crosslinks formed by site-specifically…

AnchorMS
Web

AnchorMS

A Python-coded free webtool for identifying cross-linked peptides in a sample…

A Python-coded free webtool for identifying cross-linked peptides in a sample from mass spectrometric data.

Kojak
Desktop

Kojak

A free, open-source application for efficient identification of cross-linked…

A free, open-source application for efficient identification of cross-linked peptides in a complex protein mixture. Kojak can analyze data from samples cross-linked with virtually any stable…

SIM-XL
Desktop

SIM-XL Spectrum Identification Machine for Cross-linked Peptides

A software tool that can analyze data generated through commonly used…

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…

Protein…
Desktop
Web

Protein Prospector

A software that allows comprehensive analysis of data sets by analyzing the…

A software that allows comprehensive analysis of data sets by analyzing the data at increasing levels of depth. Protein Prospector permits the detection and identification of unexpected or novel…

XLPM
Web

XLPM X-Linked Peptide Mapping Algorithm

A cross-link search algorithm. XLPM improves the speed and accuracy of the…

A cross-link search algorithm. XLPM improves the speed and accuracy of the analysis compared to other methods. The quality selection filter based on b-to-y ions ratio proved to be an effective way to…

ICC-CLASS
Desktop

ICC-CLASS Isotopically-Coded Cleavable Cross-Linking Analysis Software Suite

Analyses mass spectrometric data obtained with isotopically-coded cleavable…

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…

StavroX
Desktop

StavroX

A software which has been specifically designed for analyzing highly complex…

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…

PepSearch
Dataset

PepSearch

Scores tandem mass spectra against a peptide database, in which fragment ion…

Scores tandem mass spectra against a peptide database, in which fragment ion probabilities, number of enzymatic termini of candidate peptides, matching quality and match pattern between experimental…

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