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On the accuracy and limits of peptide fragmentation spectrum prediction.

ABSTRACT: We estimated the reproducibility of tandem mass spectra for the widely used collision-induced dissociation (CID) of peptide ions. Using the Pearson correlation coefficient as a measure of spectral similarity, we found that the within-experiment reproducibility of fragment ion intensities is very high (about 0.85). However, across different experiments and instrument types/setups, the correlation decreases by more than 15% (to about 0.70). We further investigated the accuracy of current predictors of peptide fragmentation spectra and found that they are more accurate than the ad-hoc models generally used by search engines (e.g., SEQUEST) and, surprisingly, approaching the empirical upper limit set by the average across-experiment spectral reproducibility (especially for charge +1 and charge +2 precursor ions). These results provide evidence that, in terms of accuracy of modeling, predicted peptide fragmentation spectra provide a viable alternative to spectral libraries for peptide identification, with a higher coverage of peptides and lower storage requirements. Furthermore, using five data sets of proteome digests by two different proteases, we find that PeptideART (a data-driven machine learning approach) is generally more accurate than MassAnalyzer (an approach based on a kinetic model for peptide fragmentation) in predicting fragmentation spectra but that both models are significantly more accurate than the ad-hoc models.

SUBMITTER: Li S

PROVIDER: S-EPMC3036742 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

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On the accuracy and limits of peptide fragmentation spectrum prediction.

Li Sujun S Arnold Randy J RJ Tang Haixu H Radivojac Predrag P

Analytical chemistry 20101222 3

We estimated the reproducibility of tandem mass spectra for the widely used collision-induced dissociation (CID) of peptide ions. Using the Pearson correlation coefficient as a measure of spectral similarity, we found that the within-experiment reproducibility of fragment ion intensities is very high (about 0.85). However, across different experiments and instrument types/setups, the correlation decreases by more than 15% (to about 0.70). We further investigated the accuracy of current predictor ...[more]

PMID: 21175207

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Dataset Information

On the accuracy and limits of peptide fragmentation spectrum prediction.

Publications

On the accuracy and limits of peptide fragmentation spectrum prediction.

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