Peptide Fragmentation Modeller
The Peptide Fragmentation Modeller is a simple command-line utility reads that reads in a text file of peptide sequences and generates the theoretical fragmentation pattern for each, outputting the results in .Dta files. This program computes the m/z values for the expected b and y ions. The intensity values are not predicted (all ions are assigned an intensity of 100). This program demonstrates the use of the VB.NET DLL version of the Molecular Weight Calculator to compute the theoretical peptide fragments.
Note that this software is a command line application; it does not have a graphical user interface. 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 | v1.1.3386 | Requirements | Microsoft NET Framework 1.1 |
| Date Updated | April 9, 2009 | File Size (Software Tool) | 122 KB (ZIP) |
| Registration Required | No | File size (Source Code) | 137 KB (ZIP) |
| Developers | Matthew Monroe | ||
| Comments | See the complete Revision History for a history of changes | ||
Example Results File
The following is an example .dta file created by the Peptide Fragmentation Modeller. This file contains the predicted m/z values for peptide ADNRDPASDQMK. The name assigned to the .Dta file is ADNRDPASDQMK.1347.5958396.2.dta, indicating:
- The peptide sequence: ADNRDPASDQMK
- The parent MH value: 1347.5958
- The charge state: 2+
1347.5958 2 147.1122 100 187.0719 100 278.1527 100 301.1148 100 406.2113 100 457.2159 100 521.2382 100 572.2429 100 608.2703 100 669.2956 100 679.3074 100 740.3327 100 776.3602 100 827.3647 100 891.3871 100 942.3917 100 1047.488 100 1070.45 100 1161.531 100 1201.491 100 1276.558 100 1347.596 100
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.