Software

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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.

Please Cite:
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


Please Cite:
XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking. Bioinformatics, 32(2), 2016, 306–30 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 Jan 31. [Epub ahead of print]
PMID: 22288382 [PubMed - as supplied by publisher]




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

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.
Analytical Chemistry, November 15, 2011
PMID: 21954881 [PubMed]



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.