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


pTop 2 is developed as an upgrade of pTop 1. Compared with pTop 1, pTop 2 support proteoform quantification and identifies proteoforms with unexpected modifications and cleaved or truncated proteoforms. Additionally, there are also some improvements in the precision.

pTop 1 can still be downloaded.

The main flow of pTop 2 is shown below.

Cite us

1. pTop 1.0: a High-accuracy and High-efficiency Search Engine for Intact Protein Identification.
Rui-Xiang Sun, Lan Luo, Long Wu, Rui-Min Wang, Wen-Feng Zeng, Hao Chi, Chao Liu, and Si-Min He.

Anal Chem 88, 3082-3090 (2016). [abstract]

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


You can download this file pTop2.0_user_guide.pdf, which tells you how to use pTop v2.0.

You can download this file pTop1.2_user_guide.pdf, which tells you how to use pTop v1.2.

Please read carefully the pTop Software License Agreement.

pTop v2.0 is currently free to use. Download pTop v2.0.

pTop v1.2 is currently free to use. Download pTop v1.2.

You can use example dataset to test pTop. Download example dataset.


* After installation, you need to activate the software. Just fill in some registration information when you first launch pTop and send them to to get the license file.

* If pTop expired, please redownload the software and reinstall it. Thanks for your support!

* If you have any problem, please email to: ptop[at]

Version history

Release version Release date Click for more
pTop v2.0 2019-06-18 Download Release Notes
pTop v1.2 2016-06-20 Download Release Notes