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J Proteome Res. 2013 Mar 1;12(3):1377-86. doi: 10.1021/pr301024c. Epub 2013 Jan 31.

A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.

Author information

1
Agilent Laboratories, Agilent Technologies, Santa Clara, California 95051, United States. craig.wenger@gmail.com

Abstract

The acquisition of high-resolution tandem mass spectra (MS/MS) is becoming more prevalent in proteomics, but most researchers employ peptide identification algorithms that were designed prior to this development. Here, we demonstrate new software, Morpheus, designed specifically for high-mass accuracy data, based on a simple score that is little more than the number of matching products. For a diverse collection of data sets from a variety of organisms (E. coli, yeast, human) acquired on a variety of instruments (quadrupole-time-of-flight, ion trap-orbitrap, and quadrupole-orbitrap) in different laboratories, Morpheus gives more spectrum, peptide, and protein identifications at a 1% false discovery rate (FDR) than Mascot, Open Mass Spectrometry Search Algorithm (OMSSA), and Sequest. Additionally, Morpheus is 1.5 to 4.6 times faster, depending on the data set, than the next fastest algorithm, OMSSA. Morpheus was developed in C# .NET and is available free and open source under a permissive license.

PMID:
23323968
PMCID:
PMC3586292
DOI:
10.1021/pr301024c
[Indexed for MEDLINE]
Free PMC Article
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