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

Introduction

pNovo v3.0® is an open de novo peptide sequencing algorithm using complementary HCD and ETD tandem mass spectra, which is a upgraded version of pNovo and pNovo+ and greatly improves the accuracy and the speed of de novo sequencing.

pNovo v3.0 has a great function of that it can identify unexpected modification from thousands of modifications in unimod and it highly improve the searching speed and the accuracy compared with the first two versions.

pNovo v3.0 supports the following features:

1. identifying unexpected modifications.

2. supporting the machine learning algorithm (SVM) to improve the accuracy.

3. supporting HCD and ETD spectra pairs.

4. supporting different enzymes data sets.

5. supporting multiple processes running to improve the searching speed.

6. having the search interface and result display interface.

Figure 1. Workflow of Open-pNovo. (a) Example of an original spectrum from a peptide AN(Met[H])VR, where Met[H] denotes the methylation of Histidine residue. (b) Spectrum graph (DAG) for the original spectrum. The black edges denote the normal edges, while the red ones denote the modification ones. If we do not consider the red edge, the correct peptide cannot be obtained. (c) Normal peptides and the modified peptides are obtained by finding k longest paths in DAG. (d) Score function is trained by RankBoost using three features. (e) Candidate peptides are output and sorted by the final scores, which are obtained by RankBoost. Note that when translating the original spectrum a to the spectrum graph b, each peak is translated into two vertices rather than one vertex in panel b




Supplemental Files

pNovo v3.0 is currently free to use. Download pNovo v3.0.

Notice: Please read carefully the pNovo v3.0 Software License Agreement before downloading and using the software. Please fill in the registered table and email it to pnovo@ict.ac.cn to get the registration key.

If you have any questions about it, please contact pnovo@ict.ac.cn.



Publications

Journal of Proteome Research, 9 (5), 2713–2724, 2010. [abstract]

pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra.

Hao Chi , Rui-Xiang Sun , Bing Yang , Chun-Qing Song , Leheng Wang , Chao Liu , Yan Fu , Zuo-Fei Yuan , Hai-Peng Wang , Si-Min He and Meng-Qiu Dong.


Journal of Proteome Research, 12 (2), 615-25, 2013. [abstract]

pNovo+: de novo peptide sequencing using complementary HCD and ETD tandem mass spectra.

Hao Chi , Hai-Feng Chen , Kun He , Long Wu , Bing Yang , Rui-Xiang Sun , Jian-yun Liu , Wen-Feng Zeng , Chun-Qing Song , Si-min He , Meng-Qiu Dong.



Journal of Proteome Research, 16 (2), 645–654, 2017. [abstract]

Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications.

Hao Yang, Hao Chi, Wen-Jing Zhou, Wen-Feng Zeng, Kun He, Chao Liu, Rui-Xiang Sun, and Si-Min He.