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BMC Genomics. 2010 Feb 10;11 Suppl 1:S13. doi: 10.1186/1471-2164-11-S1-S13.

Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction.

Author information

1
Sarajevo School of Science and Technology, Sarajevo, Bosnia-Herzegovina.

Abstract

BACKGROUND:

Tandem mass spectrometry (MS/MS) has become a standard method for identification of proteins extracted from biological samples but the huge number and the noise contamination of MS/MS spectra obstruct swift and reliable computer-aided interpretation. Typically, a minor fraction of the spectra per sample (most often, only a few %) and about 10% of the peaks per spectrum contribute to the final result if protein identification is not prevented by the noise at all.

RESULTS:

Two fast preprocessing screens can substantially reduce the haystack of MS/MS data. (1) Simple sequence ladder rules remove spectra non-interpretable in peptide sequences. (2) Modified Fourier-transform-based criteria clear background in the remaining data. In average, only a remainder of 35% of the MS/MS spectra (each reduced in size by about one quarter) has to be handed over to the interpretation software for reliable protein identification essentially without loss of information, with a trend to improved sequence coverage and with proportional decrease of computer resource consumption.

CONCLUSIONS:

The search for sequence ladders in tandem MS/MS spectra with subsequent noise suppression is a promising strategy to reduce the number of MS/MS spectra from electro-spray instruments and to enhance the reliability of protein matches. Supplementary material and the software are available from an accompanying WWW-site with the URL http://mendel.bii.a-star.edu.sg/mass-spectrometry/MSCleaner-2.0/.

PMID:
20158870
PMCID:
PMC2822527
DOI:
10.1186/1471-2164-11-S1-S13
[Indexed for MEDLINE]
Free PMC Article

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