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

Volume 8 Issue 5-6

Dec. 2022

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Zhiyuan Cheng, Ge Song, Yan Fu. A protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra[J]. Biophysics Reports, 2022, 8(5-6): 269-281. doi: 10.52601/bpr.2022.220024

Citation:

Zhiyuan Cheng, Ge Song, Yan Fu. A protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra[J]. Biophysics Reports, 2022, 8(5-6): 269-281. doi: 10.52601/bpr.2022.220024

Citation:

Zhiyuan Cheng, Ge Song, Yan Fu. A protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra[J]. Biophysics Reports, 2022, 8(5-6): 269-281. doi: 10.52601/bpr.2022.220024

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

doi: 10.52601/bpr.2022.220024

Zhiyuan Cheng^{1, 4},
Ge Song^{2, 3},
Yan Fu^{1, 4
,
,}

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

Funds: This study was supported by the National Natural Science Foundation of China (32070668) and the National Key R&D Program of China (2022YFA1304603, 2022YFA1004801). We are grateful to Minjia Tan and Linhui Zhai from the Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Mengqiu Dong, Adalet Memitimin and Zirui Zhao from the National Institute of Biological Sciences, Beijing, for their valuable suggestions in improving and testing PTMiner.

More Information

Corresponding author: yfu@amss.ac.cn (Y. Fu)
Received Date: 23 September 2022
Accepted Date: 27 February 2023

Available Online: 04 April 2023

Publish Date: 31 December 2022

Abstract

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.
- Modification identification,
- Open search,
- False discovery rate,
- Modification localization,
- False localization rate

Zhiyuan Cheng, Ge Song and Yan Fu declare that they have no conflict of interest.
This article does not contain any studies with human or animal subjects performed by any of the authors.

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References(11)

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