MSClustering

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Contact: Ari Frank

Summary

Tandem mass spectrometry (MS/MS) experiments often generate redundant datasets containing multiple spectra of the same peptides. Clustering of MS/MS spectra takes advantage of this redundancy by identifying multiple spectra of the same peptide and replacing them with a single representative spectrum. Analyzing only representative spectra results in significant speed-up of MS/MS database searches. We present an efficient clustering approach for analyzing large MS/MS datasets (over ten million spectra) with a capability to reduce the number of spectra submitted to further analysis by an order of magnitude. The MS/MS database search of clustered spectra results in fewer spurious hits to the database and increases number of peptide identifications as compared to regular non-clustered searches. Our open source software MS-Clustering is designed to rapidly cluster large MS/MS datasets. The program merges similar spectra (having similar m/z values – within a given tolerance), and creates a single consensus spectrum as a representative. The input formats accepted are: dta, mgf, mzXML. The output format is mgf. For more details see documentation in the downloaded zip file.