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

Introduction

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.

The paper of Open-pFind has also been uploaded to the preprint server of bioRxiv: Open-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics



Downloads

pFind 3.1.4 for windows (64bit)

- released on Nov. 21, 2018 -

Please click here to download the user manual

Notice:

* The expiration date is set on Aug. 1, 2019.

* 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. You can download it from here.

* 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: (https://github.com/pFindStudio/pFind3/issues ), see (github.pdf) for usage.





Version history

Release version Release date Download Link 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