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

We use Xtract_xml to extrat data from mzml or mzxml transformed by proteowizard by the following settings showed in pictures.
If your ProteoWizard is rather old,

System Requirements:

* Microsoft Windows operating system, Windows Vista\7\8

* Thermo Scientific Xcalibur 2.1 or a later version.

Cite us

1. 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.

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

Notice: please quote these above publications when you use pParse software in your papers.


You can download this file user_guide.pdf, which tells you how to use pParse.

pParse v2.0 is currently free to use. Please read carefully the pParse Software License Agreement before downloading and using the software. Please fill in the registered table and email it to to get the download link.

You may need to install MSFileReader(x64 or x86, according to your OS Edition) OR Thermo Scientific Xcalibur 2.2+ to extract Thermo RAW Format File.

If you have any questions about it, please contact

Version history

Release version Release date Click for more
pParse v2.0 2018-11-02 Download Release Notes