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


pFind® 3 is developed as an upgrade of pFind 2.8 (visit the old version).

Shotgun proteomics has grown rapidly in recent decades, but a large fraction of tandem mass spectrometry data in shotgun proteomics are not successfully identified. Thus we developed a novel database search algorithm, Open-pFind, to efficiently identify peptides even in an ultra-large search space which takes into account unexpected modifications, amino acid mutations, semi- or non-specific digestion and co-eluting peptides. Open-pFind has now been integrated into pFind 3 as the default workflow, and pFind 3 also supports the restricted search mode, which can be switched in the interface.

Fig. 1. Workflow of Open-pFind, including the sub-workflow of the open search module. a) The workflow of Open-pFind. MS data are first preprocessed by pParse, and then the MS/MS data are searched by the open search module. Next, the MS data are re-searched by the restricted search module against the refined search space based on the learned information in the reranking step. Finally, the results obtained from both the open and restricted searches are merged, reranked again and reported. b) The default workflow of the open search module. For each spectrum, a few tags are extracted and then searched against the indexed protein database. Peptide candidates are then generated by extending the matched tags in proteins. Finally, peptides are scored with the spectrum and ranked; the mass shift between the precursor ion and each peptide is treated as a modification and localized by testing all valid positions.

Cite us

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine.
Hao Chi, Chao Liu, Hao Yang, Wen-Feng Zeng, Long Wu, Wen-Jing Zhou, Rui-Min Wang, Xiu-Nan Niu, Yue-He Ding, Yao Zhang, Zhao-Wei Wang, Zhen-Lin Chen, Rui-Xiang Sun, Tao Liu, Guang-Ming Tan, Meng-Qiu Dong, Ping Xu, Pei-Heng Zhang, Si-Min He. Nature Biotechnology, Oct. 8, 2018.

How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data
Shao Guangcan, Cao Yong*, Chen Zhenlin, Liu Chao, Li Shangtong, Chi Hao*, Dong Meng-Qiu*. Biophysics Reports, June 30, 2021.


pFind 3.2.1 for windows (64bit)

- released on Jun. 06, 2023 -

Please click here to download the user manual


* The expiration date is set on Jan. 10, 2026.

** 尊敬的用户您好,pFind 3.2.0此次更新并不影响此前的license使用。您在下载安装之后,可以直接导入此前申请的license文件,而不用再次申请。另外,可以提前备份早期版本的ini文件以便快速替换。谢谢!

** License since version 3.2.0 is still valid for this version. After downloading and installing this version, you can just import the license applied previously instead of applying a new license. Thank you.

* If RAW file read required, MSFileReader 3.0 or a higher version need be installed first.

* .NET framework 4.5 or a higher version is required.

* JRE is also required for peptide and protein quantitation.

* pFind can support Windows 7 or higher, and the operating system should be 64-bit.

* For Windows 7 operating system, please run the setup program under administrator authority. If any one program cannot properly run after the installation, please try to right click on the program shortcut or the .exe file, and click on "Run as administrator".

Online discussion: ( ), see (github.pdf) for usage.

Version history

Release version Release date Download Link Release Notes
pFind 3.2.1 2023-06-06 Download Release Notes
pFind 3.2.0 2023-01-05 Download Release Notes
pFind 3.1.6 2020-01-02 Download Release Notes
pFind 3.1.5 2019-01-24 Download Release Notes
pFind 3.1.4 2018-11-21 Download Release Notes
pFind 3.1.3 2018-08-01 Download Release Notes
pFind 3.1.2 2018-04-10 Download Release Notes