pFind Studio: a computational solution for mass spectrometry-based proteomics
pParse™ is a software delicated to recalibrate the monoisotopic peaks of precursors in an MS/MS dataset. The basic assumption of pParse is that one tandem mass spectrum could come from more than one peptide. It could be a mixture of two or more peptides. Therefore, pParse checks the survy scan of an MS/MS spectrum ,reconstructs the eluting profile and exports the most possible precursors.
An example of co-eluted peptides on survey scans is as follow.
The mixture spectra correspoding to the co-eluted precursors above is as follow.
Now pParse+ , or pParse 2.0 is available which is 10-fold faster and more sensitive on monoisotopic peak detection. pParse+ suppurts options from command line. You can use pParse+ to convert your *.Raw into *.mgf using the switch -D as follow.
You can run pParse.exe without any option to get a detailed user guide about every switches.
pParse+ also supports parameter files. A template parameter file named "pParse.para" is with pParse+ when you decompressed it from pParse.zip. You can download the user guide to get more information on configuring the parameters.
* Microsoft Windows operating system, Windows Vista\7\8
* Thermo Scientific Xcalibur 2.1 or a later version.
If you have any problem, please email to: firstname.lastname@example.org
Proteomics, Volume 12, Issue 2, pages 226–235, No. 2 January 2012. [abstract]
Zuo-Fei Yuan, Chao Liu, Hai-Peng Wang, Rui-Xiang Sun, Yan Fu, Jing-Fen Zhang, Le-Heng Wang, Hao Chi, You Li, Li-Yun Xiu, Wen-Ping Wang, Si-Min He.