Spectral probabilities of top-down tandem mass spectra

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

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Original languageEnglish
Journal / PublicationBMC Genomics
Issue numberSupplement 1
Online published24 Jan 2014
Publication statusPublished - 2014



Background: In mass spectrometry-based proteomics, the statistical significance of a peptide-spectrum or proteinspectrum match is an important indicator of the correctness of the peptide or protein identification. In bottom-up mass spectrometry, probabilistic models, such as the generating function method, have been successfully applied to compute the statistical significance of peptide-spectrum matches for short peptides containing no posttranslational modifications. As top-down mass spectrometry, which often identifies intact proteins with posttranslational modifications, becomes available in many laboratories, the estimation of statistical significance of topdown protein identification results has come into great demand.

Results: In this paper, we study an extended generating function method for accurately computing the statistical significance of protein-spectrum matches with post-translational modifications. Experiments show that the extended generating function method achieves high accuracy in computing spectral probabilities and false discovery rates.

Conclusions: The extended generating function method is a non-trivial extension of the generating function method for bottom-up mass spectrometry. It can be used to choose the correct protein-spectrum match from several candidate protein-spectrum matches for a spectrum, as well as separate correct protein-spectrum matches from incorrect ones identified from a large number of tandem mass spectra.

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Spectral probabilities of top-down tandem mass spectra. / Liu, Xiaowen; Segar, Matthew W.; Li, Shuai Cheng; Kim, Sangtae.

In: BMC Genomics, Vol. 15, No. Supplement 1, 2014.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

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