A protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra

Zhiyuan Cheng; Ge Song; Yan Fu

doi:10.52601/bpr.2022.220024

A protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra

Biophys Rep. 2022 Dec 31;8(5-6):269-281. doi: 10.52601/bpr.2022.220024.

Authors

Zhiyuan Cheng^{1

2}, Ge Song^{3

4}, Yan Fu^{1

2}

Affiliations

¹ Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
² School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
³ Graduate School of Peking Union Medical College, Beijing 100730, China.
⁴ National Institute of Biological Sciences, Beijing, Beijing 102206, China.

Abstract

In recent years, an open search of tandem mass spectra has greatly promoted the detection of post-translational modifications (PTMs) in shotgun proteomics. However, post-processing of the results from open searches remains an unsatisfactorily resolved problem, which hinders the open search mode from wide practical use. PTMiner is a software tool based on dedicated statistical algorithms for reliable filtering, localization and annotation of the modifications (mass shifts) detected by open search. Furthermore, PTMiner also supports quality control and re-localization of modifications identified by the traditional closed search. In this protocol, we describe how to use PTMiner for the two search modes. Currently, the search engines supported by PTMiner include pFind, MSFragger, MaxQuant, Comet, MS-GF + and SEQUEST.

Keywords: False discovery rate; False localization rate; Modification identification; Modification localization; Open search.