Peptide Hit Results Processor
The Peptide Hit Results Processor can be used to convert an X!Tandem results file (XML format) or a SEQUEST Synopsis/First Hits file to a series of tab-delimited text files summarizing the results. When parsing X!Tandem data, the program will insert modification symbols into the peptide sequences for modified peptides. Parallel files are created containing sequence information, modification details, and protein information. The user can optionally provide a modification definition file that specifies the symbol to use for each modification mass.
The "Data Extraction and Analysis for LC-MS Based Proteomics" sessions at the 2007 and 2008 US HUPO conferences discussed the use of the Peptide Hit Results Processor for processing X!Tandem results. PDF files of the slides presented are available for download as a 5 MB PDF file (2007) and a 6.5 MB PDF file (2008).
Note that you can generate SEQUEST Synopsis/First Hits files from SEQUEST .Out files using the Peptide File Extractor.
Please see the Command Line Application Help page for additional information on running this program at the Windows command prompt.
| Download Software Tool | Download Source Code |
| Version | v1.1.3006 | Requirements | Microsoft NET Framework 1.1 |
| Date Updated | March 25, 2008 | File Size (Software Tool) | 324 KB (ZIP) |
| Registration Required | No | File size (Source Code) | 525 KB (ZIP) |
| Developers | Matthew Monroe | ||
| Comments | See the complete Revision History for a history of changes | ||
Example Data Files
Example X!Tandem XML Results Input File
Example Tab-Delimited Text Output File
Detailed Example Input and Output Files
- Example _xt.xml file -- X!Tandem XML results file excerpt
- Example _xt.txt file -- Tab-delimited file of X!Tandem results
- Example SeqInfo.txt file -- Sequence info file
- Example ResultToSeqMap.txt file -- Association between tab-delimited X!Tandem results file (_xt.txt) and the Sequence Info file (_SeqInfo.txt)
- Example SeqToProteinMap.txt file -- Sequence to Protein map file
Acknowledgment
All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:
Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.
