pFind Studio: a computational solution for mass spectrometry-based proteomics

Introduction

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.

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.