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Detection of co-eluted peptides using database search methods.

Alves G, Ogurtsov AY, Kwok S, Wu WW, Wang G, Shen RF, Yu YK - Biol. Direct (2008)

Bottom Line: We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides.Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev.For the full reviews, please go to the Reviewers' comments section.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA. alves@ncbi.nlm.nih.gov

ABSTRACT

Background: Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost.

Results: We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods - SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS - in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides.

Open peer review: Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.

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Related in: MedlinePlus

Example spectra of peptide co-elution. (A) and (B) are experimental spectra of two co-eluted peptides simultaneously identified by RAId_DbS, OMSSA, SEQUEST and Mascot.
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Figure 3: Example spectra of peptide co-elution. (A) and (B) are experimental spectra of two co-eluted peptides simultaneously identified by RAId_DbS, OMSSA, SEQUEST and Mascot.

Mentions: As shown in Figure 2, the probability for two peptides to share three or more peaks of the b-type and y-type is less than 5% and the probability becomes less than 1% for three randomly selected peptides to share three or more theoretical peaks. These probabilities indicate that a generated compound spectrum in general does not contain many peaks that may be used to identify several true peptides. Consequently, the identification of multiple peptides is not due to shared fragments between peptides. Two experimental spectra containing type II co-eluted peptides are shown in Figure 3. There are indeed very few b and y fragment overlaps in either spectrum, consistent with the statistics collected from our compound spectra. This experimental data, in some way, justify our compound spectra construction strategies. In both experimental spectra shown, the existence of more than one true peptide hit is confirmed by more than one search method.


Detection of co-eluted peptides using database search methods.

Alves G, Ogurtsov AY, Kwok S, Wu WW, Wang G, Shen RF, Yu YK - Biol. Direct (2008)

Example spectra of peptide co-elution. (A) and (B) are experimental spectra of two co-eluted peptides simultaneously identified by RAId_DbS, OMSSA, SEQUEST and Mascot.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483259&req=5

Figure 3: Example spectra of peptide co-elution. (A) and (B) are experimental spectra of two co-eluted peptides simultaneously identified by RAId_DbS, OMSSA, SEQUEST and Mascot.
Mentions: As shown in Figure 2, the probability for two peptides to share three or more peaks of the b-type and y-type is less than 5% and the probability becomes less than 1% for three randomly selected peptides to share three or more theoretical peaks. These probabilities indicate that a generated compound spectrum in general does not contain many peaks that may be used to identify several true peptides. Consequently, the identification of multiple peptides is not due to shared fragments between peptides. Two experimental spectra containing type II co-eluted peptides are shown in Figure 3. There are indeed very few b and y fragment overlaps in either spectrum, consistent with the statistics collected from our compound spectra. This experimental data, in some way, justify our compound spectra construction strategies. In both experimental spectra shown, the existence of more than one true peptide hit is confirmed by more than one search method.

Bottom Line: We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides.Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev.For the full reviews, please go to the Reviewers' comments section.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA. alves@ncbi.nlm.nih.gov

ABSTRACT

Background: Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost.

Results: We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods - SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS - in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides.

Open peer review: Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.

Show MeSH
Related in: MedlinePlus