Peptide File Extractor (console version)
The Peptide File Extractor will process the Sequest .Out or _out.txt files to create Synopsis and First Hits files, which are tab-delimited files summarizing the peptide identifications in the .Out file (see below for examples). If processing .Out files, then the concatenated _Out.txt file file will also be created. In addition, the program looks for .Dta files for the given dataset and will combine them into _Dta.txt files. The program can also be used as a simple .Dta file concatenator if no .Out or _Out.txt files are present for the specified dataset but .Dta files are present.
The First Hits file contains only the top scoring peptide reported for each spectrum. The Synopsis file contains all of the peptides above a threshold in each spectrum. See below for some screenshots of example input and output files. Other software on this site that reads Synopsis files includes Spectrum Look and the Peptide Hit Results Processor.
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 | v1.1.2992 | Requirements | Microsoft NET Framework 1.1 |
| Date Updated | March 11, 2008 | File Size (Software Tool) | 582 KB (ZIP) |
| Registration Required | No | File size (Source Code) | 492 KB (ZIP) |
| Developers | Matthew Monroe | ||
| Comments | See the complete Revision History for a history of changes | ||
Example Data Files
SEQUEST Out File Excerpt
SEQUEST Synopsis File Excerpt
Detailed Example Input and Output Files
- Example SEQUEST .Out files -- Search result files produced by SEQUEST
- Example Synopsis file -- Tab-delimited file of SEQUEST results, multiple peptide per spectrum
- Example First Hits file -- Tab-delimited file of SEQUEST results, one peptide per spectrum
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.
