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

Introduction

pNovoM® is a novel algorithm for de novo sequencing based on mirror peptide pair. The mirror peptide pair is defined as two peptides of the form A1A2...Al[K/R/-] and [K/R/-]A1A2...Al from trypsin and LysargiNase digestion, respectively, in which Ai denotes any one of the 20 amino acids, and "-" denotes the absence of amino acids. Nearly all of these mirror pairs contain complete product ions, resulting in precise, full-length peptide de novo sequencing.

pNovoM not only can sequence the mirror spectra pair (one from trypsin and another from LysargiNase), but also can sequence the HCD and ETD spectra. When all four spectra: trypsin-HCD, trypsin-ETD, LysargiNase-HCD and LysargiNase-ETD are considered, the recall of pNovoM can as high as 99% on the top three candidates.

pNovoM has the following features:

1. It can suport trypsin and LysargiNase spectra pairs.

2. It can support HCD and ETD spectra pairs.

3. It can support four spectra for each peptide: trypsin-HCD, trypsin-ETD, LysargiNase-HCD and LysargiNase-ETD.

4. Nearly all spectra pairs have full-complete fragment ions.

5. It can precisely sequence longer peptides than other algorithms.

6. It can effectively discriminate the first two amino acids because of existing b1 ions.

Figure 1. Mirror protease strategy for novel de novo sequencing. (a) The mirror spectra improved the quality of the matched peptide-spectrum pairs by providing a complete set of fragment ions and recognizable directions of most ions (marked with blue circles, e.g., vertices 2, 3, 4 and 5). Two dotted peaks denote that b1 and y6 were missing in the trypsin spectrum. (b) Workflow of the pNovoM algorithm based on the mirror protease strategy for de novo sequencing. Mirror spectrum pairs from trypsin- and Ac-LysargiNase-digested samples were found and twinned using pNovoM. Then, the two spectra in each pair were merged into one spectrum graph.




Supplemental Files

pNovoM is currently free to use. Download pNovoM.

Notice: Please read carefully the pNovoM 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.