Introduction

PTMiner is a software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open or close search of large-scale mass spectrometry data in proteomics.


Software

PTMiner is written in standard C++ language. Please click the link below to download the PTMiner binary release and example data:

   PTMiner Version 1.2.8 for Windows (2022.12.27)

  • Enhanced format compatibility.
  • Various minor bug fixes and improvement.

   PTMiner Version 1.2.6 for Windows (2022.03.03)

  • MaxQuant supported.
  • GUI optimized.
  • Other improvements.

   PTMiner Version 1.2.5 for Windows (2021.09.30)

  • Add summary file of modification in each step.
  • Enhanced format compatibility.

   PTMiner Version 1.2.0 for Windows (2021.03.30)

  • More search engines supported.
  • Seamless support of pFind3.
  • Option of FDR methods.
  • GUI optimized.
  • Other improvements.

   PTMiner Version 1.1.2 for Windows (2020.10.06)

   PTMiner Version 1.0.0 for Windows (2018.09.15)

   Example data

Data Sets

Simulated data
We generated the simulated data to test the performance of PTMiner. Please click the link below to download the simulated data, the open search results with pFind 2.8.5 and MODa and the PTMiner analysis results:
   Simulated data

Modification spiked-in data
We also generate the modification spiked-in data to test the performance of PTMiner. The data and its open search and PTMiner analysis results have been deposited to a full member of the ProteomeXchange consortium iProX with the dataset identifier IPX0001318000.

Synthetic peptides data
We also used the synthetic peptides data to test the performance of PTMiner. Please click the link below to download the synthetic peptides data,the open search results with pFind 2.8.5 and MODa and the PTMiner analysis results:
   Synthetic peptdies data

The draft map of human proteome
We also analyzed the draft map of human proteome. Please click the link below to download its open search results with pFind 2.8.5 and the PTMiner analysis results:
   The draft map of human proteome


Publications

Zhiwu An, Linhui Zhai, Wantao Ying, Xiaohong Qian, Fuzhou Gong, Minjia Tan and Yan Fu. PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome[J]. Molecular & Cellular Proteomics, 2019, 18(2): 391-405.

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.


Contact Us

Any problem with PTMiner or this website, please contact:

Prof. Yan Fu: yfu(at)amss(dot)ac(dot)cn