On the Relevance of Peptide Sequence Permutations in Shotgun Proteomics Studies
In collision-induced dissociation (CID) of peptides, it has been observed that rearrangement processes can take place that appear to permute/scramble the original primary structure, which may in principle adversely affect peptide identification. Here, an analysis of sequence permutation in tandem ma...
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| Veröffentlicht in: | Journal of proteome research 2011-05, Vol.10 (5), p.2409-2416 |
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| creator | Yu, Long Tan, Yanglan Tsai, Yihsuan Goodlett, David R Polfer, Nick C |
| description | In collision-induced dissociation (CID) of peptides, it has been observed that rearrangement processes can take place that appear to permute/scramble the original primary structure, which may in principle adversely affect peptide identification. Here, an analysis of sequence permutation in tandem mass spectra is presented for a previously published proteomics study on P. aeruginosa (Scherl et al., J. Am. Soc. Mass Spectrom. 2008, 19, 891) conducted using an LTQ-orbitrap. Overall, 4878 precursor ions are matched by considering the accurate mass (i.e., |
| doi_str_mv | 10.1021/pr101235w |
| format | Article |
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Here, an analysis of sequence permutation in tandem mass spectra is presented for a previously published proteomics study on P. aeruginosa (Scherl et al., J. Am. Soc. Mass Spectrom. 2008, 19, 891) conducted using an LTQ-orbitrap. Overall, 4878 precursor ions are matched by considering the accurate mass (i.e., <5 ppm) of the precursor ion and at least one fragment ion that confirms the sequence. The peptides are then grouped into higher- and lower-confidence data sets, using five fragment ions as a cutoff for higher-confidence identification. It is shown that the propensity for sequence permutation increases with the length of the tryptic peptide in both data sets. A higher charge state (i.e., 3+ vs 2+) also appears to correlate with a higher appearance of permuted masses for larger peptides. The ratio of these permuted sequence ions, compared to all tandem mass spectral peaks, reaches ∼25% in the higher-confidence data set, compared to an estimated incidence of false positives for permuted masses (maximum ∼8%), based on a null-hypothesis decoy data set.</description><identifier>ISSN: 1535-3893</identifier><identifier>EISSN: 1535-3907</identifier><identifier>DOI: 10.1021/pr101235w</identifier><identifier>PMID: 21413817</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Amino Acid Sequence - genetics ; Molecular Sequence Data ; Peptides - genetics ; Proteomics - methods ; Pseudomonas aeruginosa - chemistry ; Tandem Mass Spectrometry</subject><ispartof>Journal of proteome research, 2011-05, Vol.10 (5), p.2409-2416</ispartof><rights>Copyright © 2011 American Chemical Society</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a314t-fdaa455dd1dc25b9338fe9aed961b7d442e87499a39390164488f6fc457b5ceb3</citedby><cites>FETCH-LOGICAL-a314t-fdaa455dd1dc25b9338fe9aed961b7d442e87499a39390164488f6fc457b5ceb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/pr101235w$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/pr101235w$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,776,780,2751,27055,27903,27904,56716,56766</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21413817$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yu, Long</creatorcontrib><creatorcontrib>Tan, Yanglan</creatorcontrib><creatorcontrib>Tsai, Yihsuan</creatorcontrib><creatorcontrib>Goodlett, David R</creatorcontrib><creatorcontrib>Polfer, Nick C</creatorcontrib><title>On the Relevance of Peptide Sequence Permutations in Shotgun Proteomics Studies</title><title>Journal of proteome research</title><addtitle>J. Proteome Res</addtitle><description>In collision-induced dissociation (CID) of peptides, it has been observed that rearrangement processes can take place that appear to permute/scramble the original primary structure, which may in principle adversely affect peptide identification. Here, an analysis of sequence permutation in tandem mass spectra is presented for a previously published proteomics study on P. aeruginosa (Scherl et al., J. Am. Soc. Mass Spectrom. 2008, 19, 891) conducted using an LTQ-orbitrap. Overall, 4878 precursor ions are matched by considering the accurate mass (i.e., <5 ppm) of the precursor ion and at least one fragment ion that confirms the sequence. The peptides are then grouped into higher- and lower-confidence data sets, using five fragment ions as a cutoff for higher-confidence identification. It is shown that the propensity for sequence permutation increases with the length of the tryptic peptide in both data sets. A higher charge state (i.e., 3+ vs 2+) also appears to correlate with a higher appearance of permuted masses for larger peptides. The ratio of these permuted sequence ions, compared to all tandem mass spectral peaks, reaches ∼25% in the higher-confidence data set, compared to an estimated incidence of false positives for permuted masses (maximum ∼8%), based on a null-hypothesis decoy data set.</description><subject>Amino Acid Sequence - genetics</subject><subject>Molecular Sequence Data</subject><subject>Peptides - genetics</subject><subject>Proteomics - methods</subject><subject>Pseudomonas aeruginosa - chemistry</subject><subject>Tandem Mass Spectrometry</subject><issn>1535-3893</issn><issn>1535-3907</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNptkE1LxDAQhoMo7rp68A9ILiIeqkmTtMlRFr9gYRdXzyVtpm6XtqlJqvjv7bIfJ08zDA8v8z4IXVJyR0lM7ztHCY2Z-DlCYyqYiJgi6fF-l4qN0Jn3a0KoSAk7RaOYcsokTcdoPm9xWAF-gxq-dVsAtiVeQBcqA3gJXz1sbgtwTR90qGzrcdXi5cqGz77FC2cD2KYqPF6G3lTgz9FJqWsPF7s5QR9Pj-_Tl2g2f36dPswizSgPUWm05kIYQ00Ri1wxJktQGoxKaJ4azmOQKVdKMzV0oQnnUpZJWXCR5qKAnE3QzTa3c3Z40oesqXwBda1bsL3PZCISqZTiA3m7JQtnvXdQZp2rGu1-M0qyjb7soG9gr3apfd6AOZB7XwNwvQV04bO17V07lPwn6A_-jXbP</recordid><startdate>20110506</startdate><enddate>20110506</enddate><creator>Yu, Long</creator><creator>Tan, Yanglan</creator><creator>Tsai, Yihsuan</creator><creator>Goodlett, David R</creator><creator>Polfer, Nick C</creator><general>American Chemical Society</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20110506</creationdate><title>On the Relevance of Peptide Sequence Permutations in Shotgun Proteomics Studies</title><author>Yu, Long ; Tan, Yanglan ; Tsai, Yihsuan ; Goodlett, David R ; Polfer, Nick C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a314t-fdaa455dd1dc25b9338fe9aed961b7d442e87499a39390164488f6fc457b5ceb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Amino Acid Sequence - genetics</topic><topic>Molecular Sequence Data</topic><topic>Peptides - genetics</topic><topic>Proteomics - methods</topic><topic>Pseudomonas aeruginosa - chemistry</topic><topic>Tandem Mass Spectrometry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yu, Long</creatorcontrib><creatorcontrib>Tan, Yanglan</creatorcontrib><creatorcontrib>Tsai, Yihsuan</creatorcontrib><creatorcontrib>Goodlett, David R</creatorcontrib><creatorcontrib>Polfer, Nick C</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of proteome research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yu, Long</au><au>Tan, Yanglan</au><au>Tsai, Yihsuan</au><au>Goodlett, David R</au><au>Polfer, Nick C</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>On the Relevance of Peptide Sequence Permutations in Shotgun Proteomics Studies</atitle><jtitle>Journal of proteome research</jtitle><addtitle>J. Proteome Res</addtitle><date>2011-05-06</date><risdate>2011</risdate><volume>10</volume><issue>5</issue><spage>2409</spage><epage>2416</epage><pages>2409-2416</pages><issn>1535-3893</issn><eissn>1535-3907</eissn><abstract>In collision-induced dissociation (CID) of peptides, it has been observed that rearrangement processes can take place that appear to permute/scramble the original primary structure, which may in principle adversely affect peptide identification. Here, an analysis of sequence permutation in tandem mass spectra is presented for a previously published proteomics study on P. aeruginosa (Scherl et al., J. Am. Soc. Mass Spectrom. 2008, 19, 891) conducted using an LTQ-orbitrap. Overall, 4878 precursor ions are matched by considering the accurate mass (i.e., <5 ppm) of the precursor ion and at least one fragment ion that confirms the sequence. The peptides are then grouped into higher- and lower-confidence data sets, using five fragment ions as a cutoff for higher-confidence identification. It is shown that the propensity for sequence permutation increases with the length of the tryptic peptide in both data sets. A higher charge state (i.e., 3+ vs 2+) also appears to correlate with a higher appearance of permuted masses for larger peptides. The ratio of these permuted sequence ions, compared to all tandem mass spectral peaks, reaches ∼25% in the higher-confidence data set, compared to an estimated incidence of false positives for permuted masses (maximum ∼8%), based on a null-hypothesis decoy data set.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>21413817</pmid><doi>10.1021/pr101235w</doi><tpages>8</tpages></addata></record> |
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| language | eng |
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| source | MEDLINE; ACS Publications |
| subjects | Amino Acid Sequence - genetics Molecular Sequence Data Peptides - genetics Proteomics - methods Pseudomonas aeruginosa - chemistry Tandem Mass Spectrometry |
| title | On the Relevance of Peptide Sequence Permutations in Shotgun Proteomics Studies |
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