msgfdb2pepxml

Copyright Notice

msgfdb2pepxml is Copyright © 2011 Boris Nagaev, Ksenia Yashina and Magnus Palmblad.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.

You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

About msgfdb2pepxml

msgfdb2pepxml is a Python program that converts output from the MS-GFDB search engine to pepXML. It includes several functions that may be useful in conversion of other data formats to pepXML, mzIdentML or similar. Among these are regular expressions that recognize which enzyme was used and with what specificity (i.e. the cleavage rules and "fidelity" attribute in pepXML) from a set of peptide sequences. msgfdb2pepxml will always try to generate the most restrictive enzyme and specificity that matches all peptides. All enzymes and non-enzymatic cleavage agents included in the PSI-MS controlled vocabulary version 3.10 (2011-08-24) are supported. The converter also recalculates peptide and post-translational modification masses with arbitrary precision and populates the pepXML file with these and other information that can be derived from the MS-GFDB output file, such as chromatographic retention times.

msgfdb2pepxml requires Python 2.7.
Download msgfdb2pepxml.py (version 2.0)

Using msgfdb2pepxml

List of options: Usage:

python msgfdb2pepxml.py -i <MS-GFDB output> [-c <MS-GFDB configuration (modifications)> -s <source data (in mzXML)> -o <pepXML file to write> -f <FASTA database file>]

Example:

Click on the links in the command to see input file "example.msgfdb", configuration file "Mods.txt" and corresponding output file "example.pep.xml":

python msgfdb2pepxml.py -i example.msgfdb -c Mods.txt -o example.pep.xml