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


pCluster is a software tool for detecting protein modifications by tandem mass spectra clustering.

It contains two algorithms, one of which clusters spectra using precursor information and the other uses fragment information in LC-MS/MS. The precursor-based algorithm named DeltAMT can detect abundant modifications in an extremely fast speed.

pCluster is currently used to detect abundant modifications. To detect low-abundance modifications, please try our another tool, pMatch.


pCluster was written in C++ and can be downloaded for non-commercial use:


* UserGuide.pdf

The DeltAMT algorithm was also implemented using MATLAB:


Usage: deltamt para_file


1, run the above command in MS DOS window.

2, para_file is a parameter file (an example: example_para.txt)

3, MATLAB (or running environment) must be installed. [download...]

4, Bioworks must be installed to read Thermo Scientific’s RAW file.


Molecular & Cellular Proteomics, 2011, 10(5). [abstract]

DeltAMT: A Statistical Algorithm for Fast Detection of Protein Modifications From LC-MS/MS Data.

Yan Fu, Li-Yun Xiu, Wei Jia, Ding Ye, Rui-Xiang Sun, Xiao-Hong Qian, and Si-Min He.