Software

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XLinkProphet - Software for increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks.
Download XLinkProphet

This program validates search results of XL-MS cleavable cross-linked peptides.

Increased Sensitivity with Automated Validation of XL-MS Cleavable Peptide Crosslinks. Bioinformatics, bty720, https://doi.org/10.1093/bioinformatics/bty720.


ReACT2prm - Software for calculation of PRM transitions for PIR cross-linked peptide pairs.
Download ReACT2prm

This program takes a react2.xls file as input and creates a tab-delimited output file suitable for Skyline import for PRM analysis. The resulting file will have a *.react2.skyline.txt extension.

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. PLoS One. 2016 Dec 20;11(12):e0167547. doi: 10.1371/journal.pone.0167547


PIR Spectral Libraries for use with SpectraST.
Acinetobacter baumannii: Download .zip file.
Saccharomyces cerevisiae: Download .zip file.
Klebsiella pneuomonia: Download .zip file.

XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.
Download (latest): Version 0.2.1
Download: Version 0.1.4 Version 0.1.3


XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking. Bioinformatics, 32(2), 2016, 306-8 DOI: 10.1093/bioinformatics/btv519.

For questions or comments please email:
Devin Schweppe (dkschwep at uw.edu)

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To install package in R:
install.packages("C:/path_to_XLmap_tar_file/XLmap_0.2.1.tar.gz",repos=NULL,type="source")


Implementation of XLmap.
  • The tarball package can be loaded based on the source file using:
    • >install.packages("C:/path_to_XLmap_tar_file/XLmap_0.2.1.tar.gz",repos=NULL, type=”source”)
  • Dependencies and imports for XLmap:
      • i. R version: >2.0.1
      ii. Packages:
      • Rpdb
      • lattice
      • latticeExtra
      • Matrix
      • tcltk
      • zoo
  • Note: If your PDB/PDBx file does not have chainids (i.e. blank values in 'chainid' column) then specify which.chain="".

    • Definition of function inputs and options.
    Defaults:
    >contactmap=function(cadistance,
      proteininput,
      molfile=NULL,
      xltable=NULL,
      pdbx=FALSE,
      cm.offset=0,
      sites.only=FALSE,
      which.chain=’A’)
    >cmscore=function(distancerange,
      proteininput,
      molfile=NULL,
      xltable=NULL,
      cms.pdbx=FALSE,
      cms.offset=0,
      cms.sites.only=FALSE,
      cms.which.chain=’A’)
    Options:
    molfile= file_path Path to PDB or PDBx/mmCIF file.

    xltable= file_path Path to file containing sites of protein crosslinks.

    sites.only/cms.sites.only=TRUE Allows the user to input XL-MS data as a two column data.frame only containing site information for a single protein (i.e. ‘mod_pos1’ and ‘mod_pos2’).

    pdbx/cms.pdbx=TRUE Allows the user to input structural information from a PDBx/mmCIF file instead of a PDB file.

    cm.offset/cms.offset=n Allows the user to impose an offset of n residues to compensate for differences between residue numbers in a structure versus those in the XL-MS data.
      Example: an N terminal HA-tag increases the residue number of all residues in the crystal structure by 9, therefore the user can set cm.offset=9.
    which.chain/cms.which.chain=’*’ Allows selection of specific amino acid chains (A-Z) from within the PDB file.

FT-ARM - Tool for identification and quantification of multiplexed high-resolution data.
Download FT-ARM

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification.
Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE., J Proteome Res. 2012 Mar 2;11(3):1621-32. doi: 10.1021/pr2008175. Epub 2012 Feb 21. PMID: 22288382

BLinks - Software for the analysis and visualization of data generated using Protein Interaction Reporter (PIR) technology.
Download BLinks

Improved strategies for rapid identification of chemically cross-linked peptides using protein interaction reporter technology., Michael R. Hoopmann, Chad R. Weisbrod, James E. Bruce, J Proteome Res. 2010 Dec 3;9(12):6323-33. doi: 10.1021/pr100572u. Epub 2010 Nov 10. PMID: 20886857

SILACtor - Software for automated protein turnover analysis and method refinement for SILAC data.
Download SILACtor

SILACtor: software to enable dynamic SILAC studies., Hoopmann MR, Chavez JD, Bruce JE, Anal Chem. 2011 Nov 15;83(22):8403-10. doi: 10.1021/ac2017053. Epub 2011 Oct 27. PMID: 21954881

Log_file_getter - Software for automated extraction of LTQ Velos-FT logfile info.
Download Log_File_Getter

Extract LTQ Velos .log file output from ReACT, DIFR, and future ITCL development output.

ReACT_STAT - Software for statistical breakdown of ReACT cross-linking analysis.
Download ReACT_STAT

ReACT_STAT calculates statistics and provides automated analysis on ReACT cross-linked peptide samples to assess the quality of the experiment.

Mango - A tool for facilitating the search of CID-cleavable cross-linking data.
Download Mango binaries
Source code

This program takes an .mzXML and outputs a modified .ms2 or .mgf file with individual peptide masses for search with Comet or other search tools.

Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification. Anal Chem. 2018 Apr 20. doi:10.1021/acs.analchem.7b04991. PubMed PMID: 29676898.