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MS Data Miner

MS Data Miner - A web-based proteomics software

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Data processing and analysis in proteomic studies is a significant challenge and very time consuming. MS Data Miner (MDM) is a freely available web-based software to analyze, process, validate, compare, and display output files from MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science) and ProteinPilot (AB Sciex). It was developed to significantly decrease the data analysis time and to handle large proteomic studies.

This open sourced system includes a spectra validation-system and automatically screenshot generation tool for Mascot-assigned spectra. In addition, a GO term analysis function and a tool for generating comparative data-reports are included.

The software is described in the following paper:
Dyrlund TF, Poulsen ET, Scavenius C, Sanggaard KW, Enghild JJ. MS Data Miner: A web-based software tool to analyze, compare and share mass spectrometry protein identifications. PROTEOMICS 2012

MS Data Miner Web Site


  • Import MS data from Mascot, Mascot Distiller, ProteinPilot and UniProt
  • Support for SILAC and iTRAQ data
  • Spectra validation of Mascot assigned spectra
  • Screenshot generation of Mascot assigned spectra
  • GO term and GO slim category analysis
  • Comparative data report generation
  • Venn diagram creator
  • Easy sharing and access to data
  • SRM selector with Skyline method creator


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