DeconMSn
DeconMSn creates spectrum files for tandem mass spectrometry data. It can read Thermo Finnigan .Raw files (though you must separately install Xcalibur to obtain the required DLLS). Alternatively, the input data can be in the mzXML format. The program can process data from low resolution instruments (e.g. LCQ or LTQ) and from high resolution instruments (e.g. LTQ-FT or LTQ-Orbitrap).
With high resolution data, for each MS/MS spectrum the parent monoisotopic mass is accurately calculated from the parent isotopic distribution using a modified THRASH approach (see the DeconMSn tutorial below and the Decon2LS tutorial). For low-resolution data, DeconMSn uses a support-vector machine based charge-detection algorithm to determine parent mass.
Results are stored as either .Dta files or .MGF files, which can be then used for peptide identifications using search engines such as SEQUEST, X!Tandem or MASCOT (see Matrix Science's Data File Format page for additional descriptions of these file types). Additional details on the DeconMSn software are available in the 2007 ASMS poster and in a Supplementary Info / Tutorial Powerpoint file (764 KB).
Please note that the nature of the distribution of correct identifications to wrong identifications is substantially affected by the use of DeconMSn. Thus, caution must be exercised while using tools such as Peptide Prophet that are trained on differing distributions
Please see the Command Line Application Help page for additional information on running this program at the Windows command prompt.
| Download Software Tool | Download Tutorial | Download Source Code | Download MatLab SVM Scripts |
| Version | v2.1 | Requirements | Microsoft NET Framework 1.1 |
| Date Updated | May 1, 2008 | File Size (Software Tool) | 2.5 MB (ZIP) |
| Registration Required | No | File size (Source Code) | 15.4 MB (ZIP) |
| Developers | Anoop Mayampurath and Navdeep Jaitly | ||
| Comments | See the complete Revision History for a history of changes | ||
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.
Processing Example
The following shows the parent ion and fragmentation spectra for an example peptide from an analysis of a Shewanella oneidensis sample. DeconMSn processed each MS2 spectrum in the input file to determine the accurate mass and charge state of the parent ion in the preceding MS1 spectrum. If the isotopic envelope of the parent ion is too low in intensity to determine the parent ion's mass and charge, then the two preceding MS1 spectra and the two following MS1 spectra are summed together (5 spectra total), and then the deisotoping procedure is repeated.
Isotopic envelope
Isotopic envelope in an example MS1 spectrum
Deisotoping Result
Deisotoping result (view from Decon2LS, which uses the same deisotoping algorithm as DeconMSn)
Fragmentation spectrum
Fragmentation spectrum data (MS/MS) that corresponds to the MS1 spectrum shown above
Example DTA File
Example DTA file created by DeconMSn (view the complete file)
Peptide ID determined by analysis with SEQUEST:
K.LQEAVDKGLYNPFVEGGNATQATLDTFLHTATR.K
XCorr: 8.06
DelCN: 0.58
Example Parameter File
DeconMSn supports using the -P switch to specify an XML parameter file that defines the processing options. View the example parameter file.
