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.
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)