Comet search engine#

Comet [ENG2012] is an open source tandem mass spectrometry (MS/MS) sequence database search tool released under the Apache 2.0 license [ENG2015]. Among some of the main features of the algorithm are: multithreading, speed and memory allocation.

Note

In quantms, comet has proved to be faster compare with MS-GF+ peptide search engine while identifying less than 15% PSMs. In addition, comet consume less memory than MS-GF+ peptide search engine in general, while consuming more CPU.

_images/resources-search-engine.png

In quantms, PSMs are exported from the search engine into .idXML (read more Formats in quantms) without filtering for the re-scoring (see Peptide identification from fragment spectra) step with percolator. The pipeline stores these original file results in the result folder under searchenginecomet.

References#

[ENG2012]

Comet: an open source tandem mass spectrometry sequence database search tool. Eng JK, Jahan TA, Hoopmann MR. Proteomics. 2012 Nov 12. doi: 10.1002/pmic.201200439

[ENG2015]

A Deeper Look into Comet - Implementation and Features. Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. J Am Soc Mass Spectrom. 2015 Jun 27. doi: 10.1007/s13361-015-1179-x