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 You can download the user guide to get more information on configuring the parameters.

Supplemental Files

pParse+ is free to use. Send a request email to or and you will recieve the download link.

System Requirements:

* 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:


Proteomics, Volume 12, Issue 2, pages 226–235, No. 2 January 2012. [abstract]

pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra.

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.