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Update (01 Nov 2012): a new and improved web-based version of MsClust can be accessed on a Galaxy site upon request. Contact Pieter Lukasse for more details.

MSClust is a C++ GUI application developed for windows platform. However you need to install a Borland Builder development environment in order to execute this application. The current package comes with set of files in a directory (GUI_proj) includes msclust.cpp ( main C++ program), .bpr (borland project file) and other library files that are required to run this project.

Operating steps: 1. Double click on pmsclust.exe or alternately type pmsclust.exe in command window from within the directory. You can directly type pmsclust.exe in command window if you set the path. It opens a window :


As you can see above, the required values are loaded by default into the fields. (they are predefined in MsClustClass.cpp file that is located in the same directory where pmsclust.exe is present)

2. Click on OpenFile button Select the input file from the disk. The input file for the MSClust is the output generated by Metalign/Metot tools. This is .txt file (tab delimited )

Example file is shown below.


This file contains the information about the Scan number, Retention Time, Mass, and intensities of the samples.

As soon you select the file, the program reads the file and displays Number of samples, and Number of mass Peaks present in the input file.


3. After you selecting the file, the OK button in the window is highlighted. Click on it. Then program calculates Potential Density Field. And then it performs Centrotype selection and mass peak classification.

4. Notifies when the job is done. 6 output files will be generated and saved into the folder from where you have selected the input file. i. Centrotypes.txt ii. Classification.txt iii. Parameters.txt iv. Tic.txt v. Sim.txt vi. Mass_spectra.msp

Centrotypes.txt is a tab delimited file.

MSC-4.jpg MSC-5.jpg MSC-6.jpg

parameters.txt is a plain text file



Go to NMC

Go to NMC DSP data Processing Tool Chain