Detection of co-eluted peptides using database search methods
<p>Abstract</p> <p>Background</p> <p>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 iden...
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| Format: | Article |
| Language: | English |
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BMC
2008-07-01
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| Series: | Biology Direct |
| Online Access: | http://www.biology-direct.com/content/3/1/27 |
| _version_ | 1811278676798472192 |
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| author | Wang Guanghui Wu Wells W Kwok Siwei Ogurtsov Aleksey Y Alves Gelio Shen Rong-Fong Yu Yi-Kuo |
| author_facet | Wang Guanghui Wu Wells W Kwok Siwei Ogurtsov Aleksey Y Alves Gelio Shen Rong-Fong Yu Yi-Kuo |
| author_sort | Wang Guanghui |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 (MS<sup>2</sup>) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost.</p> <p>Results</p> <p>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 MS<sup>2 </sup>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.</p> <p>Open peer review</p> <p>Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.</p> |
| first_indexed | 2024-04-13T00:40:04Z |
| format | Article |
| id | doaj.art-abb9691ce76a4079badd514e7a220933 |
| institution | Directory Open Access Journal |
| issn | 1745-6150 |
| language | English |
| last_indexed | 2024-04-13T00:40:04Z |
| publishDate | 2008-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Biology Direct |
| spelling | doaj.art-abb9691ce76a4079badd514e7a2209332022-12-22T03:10:13ZengBMCBiology Direct1745-61502008-07-01312710.1186/1745-6150-3-27Detection of co-eluted peptides using database search methodsWang GuanghuiWu Wells WKwok SiweiOgurtsov Aleksey YAlves GelioShen Rong-FongYu Yi-Kuo<p>Abstract</p> <p>Background</p> <p>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 (MS<sup>2</sup>) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost.</p> <p>Results</p> <p>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 MS<sup>2 </sup>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.</p> <p>Open peer review</p> <p>Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.</p>http://www.biology-direct.com/content/3/1/27 |
| spellingShingle | Wang Guanghui Wu Wells W Kwok Siwei Ogurtsov Aleksey Y Alves Gelio Shen Rong-Fong Yu Yi-Kuo Detection of co-eluted peptides using database search methods Biology Direct |
| title | Detection of co-eluted peptides using database search methods |
| title_full | Detection of co-eluted peptides using database search methods |
| title_fullStr | Detection of co-eluted peptides using database search methods |
| title_full_unstemmed | Detection of co-eluted peptides using database search methods |
| title_short | Detection of co-eluted peptides using database search methods |
| title_sort | detection of co eluted peptides using database search methods |
| url | http://www.biology-direct.com/content/3/1/27 |
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