Ulrich's Proteomics Toolbox

All the tools run within your browser, no files are transfered to the server!

PepXML filtering for N₁₁₅-X-S/T sequence motifs

filters your .pep.xml file for peptides with a N₁₁₅-X-S/T sequence motif

ProtXML filtering for N₁₁₅-X-S/T sequence motifs

filters your .prot.xml file for proteins with peptides with a N₁₁₅-X-S/T sequence motif

• This tool just removes non-matching peptide entries for every protein but does NOT re-calculate protein-level summaries like probability, coverage, spectral counts, etc.
• A peptide with a deamidated Asp at the last or second to last position cannot be matched to the N-X-S/T motif and therefore will be filtered out.

PepXML sample merging

If you interacted multiple samples to one pep.xml file, this tool merges the sample entries in your interacted .pep.xml file for complete matching with ProGenesis software. Moreover, xcorr scores will be replaced with with corresponding PeptideProphet probabilities so that you are able to filter for probabilities in ProGenesis.

In case your pep.xml file is too large for processing in the browser, you can also process a file using this perl script: perl -0777 -pe "s|</msms_run_summary>.*?<spectrum_query|<spectrum_query|gs" interact.pep.xml > interact.progenesis.pep.xml

To replace the xcorr scores with corresponding PeptideProphet probabilities, use this perl script on a Linux system (including Mac): perl -0777 -pe "s|(<search_score name=\"xcorr\" value=\")[\.\d]+(.*?<peptideprophet_result probability=\")([\.\d]+)|\1\3\2\3|gs" interact.progenesis.pep.xml > interact.progenesisProb.pep.xml ...or this perl script on a Windows system: perl -0777 -pe "s|(<search_score name=\""xcorr\"" value=\"")[\.\d]+(.*?<peptideprophet_result.probability=\"")([\.\d]+)|\1\3\2\3|gs" interact.progenesis.pep.xml > interact.progenesisProb.pep.xml

PepXML add retention times

add retention time to your .pep.xml files using ProteoWizard msaccess output

• You have to run msaccess -x spectrum_table *.mzXML first to generate a .spectrum_table.txt for each of your mzML/mzXML files.
• In the dialog, select all of these .spectrum_table.txt files and also all of the corresponding .pep.xml files.
• Do not run on interacted .pep.xml files.
• Do not run on .pep.xml files which already have RT info.

PepXML to TSV

converts a .pep.xml file to tabular format (tab-separated values file) for analysis in MS Excel or R

Spectral Histograms

reads an .ms1 or .ms2 file (see msconvert) and calculates a binned histogram of all peaks

created by Ulrich Omasits, 2013/2014

compatibility: Chrome (from version 8), Firefox (from version 4), Internet Explorer (from version 10), Opera (from version 15), Safari (untested!)