Introduction

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


Software

PTMiner is written in standard C++ language. The source code of PTMiner is available on request, and will be deposited to a community repository soon. Please click the link below to download the PTMiner 1.0 binary release:
   PTMiner Version 1.0 for Windows

Notes:

  v1.0 Release (2017.07)

 ---- This version owns a GUI written in C# language.

---- There is a user guide for this software tool.

---- Download the test data here.

The Extended Ascore is written in Matlab. Please click the link below to download the source code:
   The extended Ascore code


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

An, Z.; Fu, Y.; Ying, W.; Qian, X.; Gong, F., A probabilistic iterative algorithm for unrestrictive protein modification localization. In 63rd ASMS Conference of Mass Spectrometry and Allied Topics, St. Louis, United States, 2015.

An, Z.; Fu, Y.; Gong, F. Unrestrictive protein modification localization and quality control for open search of mass spectra, ChemRxiv. https://doi.org/10.26434/chemrxiv.5797995.v1 (2018)


About Us

Our research focuses on algorithm and software development for MS-based proteomics. For more information, please visit our website.

Our affiliation:
   Academy of Mathematics and Systems Science , Chinese Academy of Sciences


Contact Us

Address: No.55 Zhongguancun East Road,
               Haidian District, Beijing, China
Postcode: 100190

Any problem with PTMiner or this website, please contact:

Zhi-Wu An: anzhwu12@mails.ucas.ac.cn

Yan Fu: yfu@amss.ac.cn