A graph-theoretic approach for the separation of b and y ions in tandem mass spectra

@article{Yan2005AGA,
  title={A graph-theoretic approach for the separation of b and y ions in tandem mass spectra},
  author={Bo Yan and Chongle Pan and Victor Olman and Robert L. Hettich and Ying Xu},
  journal={Bioinformatics},
  year={2005},
  volume={21 5},
  pages={
          563-74
        }
}
MOTIVATION Ion-type identification is a fundamental problem in computational proteomics. Methods for accurate identification of ion types provide the basis for many mass spectrometry data interpretation problems, including (a) de novo sequencing, (b) identification of post-translational modifications and mutations and (c) validation of database search results. RESULTS Here, we present a novel graph-theoretic approach for solving the problem of separating b ions from y ions in a set of tandem… 
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38 Citations
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Methods Citations
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38 Citations

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References

SHOWING 1-10 OF 34 REFERENCES
A Suboptimal Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry
TLDR
This work gives the first polynomial time suboptimal algorithm that finds all theSuboptimal solutions (peptides) in O(p|E|) time, where p is the number of solutions.
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry
TLDR
The de novo peptide sequencing problem is to reconstruct the peptide sequence from a given tandem mass spectral data of k ions by implicitly transforming the spectral data into an NC-spectrum graph G (V, E) where /V/ = 2k + 2, and this approach can be further used to discover a modified amino acid in O(/V//E/) time.
De Novo Peptide Sequencing via Tandem Mass Spectrometry
TLDR
A new algorithm, SHERENGA, is developed for de novo interpretation of MS/MS spectral interpretation that automatically learns fragment ion types and intensity thresholds from a collection of test spectra generated from any type of mass spectrometer.
Mutation-tolerant protein identification by mass-spectrometry
TLDR
A new notion of spectral similarity is introduced that allows one to identify related spectra even if the corresponding peptides have multiple modifications/mutations, and a new algorithm for mutation-tolerant database search as well as a method for cross-correlating related uncharacterized spectra.
Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry.
There are several computer programs that can match peptide tandem mass spectrometry data to their exactly corresponding database sequences, and in most protein identification projects, these programs…
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
TLDR
Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies.
Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides.
TLDR
An examination of 1465 ion trap spectra from doubly charged tryptic peptides reveals several trends important to understanding this fragmentation process, including fragment ions corresponding to a formal loss of ammonia appear preferentially in peptides containing Gln and Asn.
Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database.
TLDR
The approach described in this paper provides a convenient method to match the nascent tandem mass spectra of modified peptides to sequences in a protein database and thereby identify previously unknown sites of modification.
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
TLDR
MudPIT was applied to the proteome of the Saccharomyces cerevisiae strain BJ5460 grown to mid-log phase and yielded the largest proteome analysis to date, identifying 131 proteins with three or more predicted transmembrane domains which allowed us to map the soluble domains of many of the integral membrane proteins.
...
...