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Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: Case study using a whole cell digest of Clostridium thermocellum
We have developed a real‐time graphic‐processor‐unit‐based search engine capable of high‐quality peptide identifications in
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| Published in: | Proteomics (Weinheim) 2012-04, Vol.12 (8), p.1160-1169 |
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| Main Authors: | , , , , , , |
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| Language: | English |
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| container_end_page | 1169 |
| container_issue | 8 |
| container_start_page | 1160 |
| container_title | Proteomics (Weinheim) |
| container_volume | 12 |
| creator | McQueen, Peter Spicer, Vic Rydzak, Thomas Sparling, Richard Levin, David Wilkins, John A. Krokhin, Oleg |
| description | We have developed a real‐time graphic‐processor‐unit‐based search engine capable of high‐quality peptide identifications in |
| doi_str_mv | 10.1002/pmic.201100425 |
| format | article |
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The steps of peptide/protein identification, in‐silico prediction of all possible tryptic peptides from these proteins, and the prediction of their expected retention times and m/z values take less than 5 s per cycle over ∼3000 MS/MS spectra. This lays the foundation for information‐dependent acquisition with exclusion lists generated on‐the‐fly, as the instrument continues to acquire data. While a complete evaluation of the dynamic exclusion system requires the participation from instrument vendors, we conducted a series of model experiments using a whole cell tryptic digestion of the bacterium Clostridium thermocellum. We ran a series of five iterative LC‐MS/MS runs, adding a new exclusion list at each of four chromatographic “tripping points” – the elution times of the four standard peptides spiked into the sample. Retention times of these standard peptides were also used for real‐time “chromatographic calibration.” The dynamic exclusion approach gave a ∼5% increase in confident protein identification (for typical 2 h LC‐MS/MS run), and reduced the average number of identified peptides per protein from 4.7 to 2.9. Its application to a two‐times shorter gradient gave a ∼17% increase in proteins identified. Further improvements are possible for instruments with better mass accuracy, by employing a more accurate retention prediction algorithm and by developing better understanding of the possible chemical modifications and fragmentations produced during electrospray ionization.</description><identifier>ISSN: 1615-9853</identifier><identifier>EISSN: 1615-9861</identifier><identifier>DOI: 10.1002/pmic.201100425</identifier><identifier>PMID: 22577018</identifier><language>eng</language><publisher>Germany: Blackwell Publishing Ltd</publisher><subject>Algorithms ; Automatic Data Processing ; Chromatography, Liquid - methods ; Clostridium thermocellum ; Clostridium thermocellum - chemistry ; Information-dependent acquisition ; Peptide retention prediction ; Peptides - analysis ; Proteomics - methods ; Reference Standards ; Reproducibility of Results ; RP HPLC ; Shotgun proteomics ; Software ; Tandem Mass Spectrometry - methods ; Technology ; Time Factors ; Trypsin - chemistry</subject><ispartof>Proteomics (Weinheim), 2012-04, Vol.12 (8), p.1160-1169</ispartof><rights>2012 WILEY‐VCH Verlag GmbH & Co. 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KGaA, Weinheim</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,777,781,27905,27906</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22577018$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>McQueen, Peter</creatorcontrib><creatorcontrib>Spicer, Vic</creatorcontrib><creatorcontrib>Rydzak, Thomas</creatorcontrib><creatorcontrib>Sparling, Richard</creatorcontrib><creatorcontrib>Levin, David</creatorcontrib><creatorcontrib>Wilkins, John A.</creatorcontrib><creatorcontrib>Krokhin, Oleg</creatorcontrib><title>Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: Case study using a whole cell digest of Clostridium thermocellum</title><title>Proteomics (Weinheim)</title><addtitle>Proteomics</addtitle><description>We have developed a real‐time graphic‐processor‐unit‐based search engine capable of high‐quality peptide identifications in <500 μs per spectrum. The steps of peptide/protein identification, in‐silico prediction of all possible tryptic peptides from these proteins, and the prediction of their expected retention times and m/z values take less than 5 s per cycle over ∼3000 MS/MS spectra. This lays the foundation for information‐dependent acquisition with exclusion lists generated on‐the‐fly, as the instrument continues to acquire data. While a complete evaluation of the dynamic exclusion system requires the participation from instrument vendors, we conducted a series of model experiments using a whole cell tryptic digestion of the bacterium Clostridium thermocellum. We ran a series of five iterative LC‐MS/MS runs, adding a new exclusion list at each of four chromatographic “tripping points” – the elution times of the four standard peptides spiked into the sample. Retention times of these standard peptides were also used for real‐time “chromatographic calibration.” The dynamic exclusion approach gave a ∼5% increase in confident protein identification (for typical 2 h LC‐MS/MS run), and reduced the average number of identified peptides per protein from 4.7 to 2.9. Its application to a two‐times shorter gradient gave a ∼17% increase in proteins identified. Further improvements are possible for instruments with better mass accuracy, by employing a more accurate retention prediction algorithm and by developing better understanding of the possible chemical modifications and fragmentations produced during electrospray ionization.</description><subject>Algorithms</subject><subject>Automatic Data Processing</subject><subject>Chromatography, Liquid - methods</subject><subject>Clostridium thermocellum</subject><subject>Clostridium thermocellum - chemistry</subject><subject>Information-dependent acquisition</subject><subject>Peptide retention prediction</subject><subject>Peptides - analysis</subject><subject>Proteomics - methods</subject><subject>Reference Standards</subject><subject>Reproducibility of Results</subject><subject>RP HPLC</subject><subject>Shotgun proteomics</subject><subject>Software</subject><subject>Tandem Mass Spectrometry - methods</subject><subject>Technology</subject><subject>Time Factors</subject><subject>Trypsin - chemistry</subject><issn>1615-9853</issn><issn>1615-9861</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><recordid>eNqFkk9v1DAQxSMEoqVw5YgsceGS1n_iOOaGIigrdpeVCkLiYrnxeNfFidM40Xa_Dp8UR1v2wIXTeDS_N3rWvCx7TfAlwZhe9a1rLikmqSkof5Kdk5LwXFYleXp6c3aWvYjxDmMiKimeZ2eUciEwqc6z34vOhqHVowtdbqCHzkA3omWdr26uVjdIN_eTi24eo70bdwgeGj_FufUujhH1YUwCp70_oC10MOgRDErLxh3k1h_eo1pHQHGczAElYbdFGu13wQNqwHtk3BbiiIJFtQ9xHJxxU4uSeGjDDEzty-yZ1T7Cq8d6kX3_9PFb_Tlffr1e1B-WuWOci9xaLS3TppSaGGNBlFUhBYfCNCU2GgQDIJUojLYUpMUNlfw2VUlLzKgl7CJ7d9zbD-F-SqZU6-JsQXcQpqgIp1JyUVHxfxQTKopKViyhb_9B78I0dOkjaSERRVFWUibqzSM13bZgVD-4Vg8H9fdQCSiOwN55OJzmBKs5BmqOgTrFQG1Wi1pgNhvNj7J0K3g4yfTwS5WCCa5-rK_VZk3o-gvfqJ_sD1lZtyg</recordid><startdate>201204</startdate><enddate>201204</enddate><creator>McQueen, Peter</creator><creator>Spicer, Vic</creator><creator>Rydzak, Thomas</creator><creator>Sparling, Richard</creator><creator>Levin, David</creator><creator>Wilkins, John A.</creator><creator>Krokhin, Oleg</creator><general>Blackwell Publishing Ltd</general><general>Wiley Subscription Services, Inc</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7QL</scope><scope>C1K</scope></search><sort><creationdate>201204</creationdate><title>Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: Case study using a whole cell digest of Clostridium thermocellum</title><author>McQueen, Peter ; Spicer, Vic ; Rydzak, Thomas ; Sparling, Richard ; Levin, David ; Wilkins, John A. ; Krokhin, Oleg</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-i3557-ffa9f3ad69a1ddfe7684975e4dc60dae73ee1874daf2e9f0c295b9f0926032f13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Algorithms</topic><topic>Automatic Data Processing</topic><topic>Chromatography, Liquid - methods</topic><topic>Clostridium thermocellum</topic><topic>Clostridium thermocellum - chemistry</topic><topic>Information-dependent acquisition</topic><topic>Peptide retention prediction</topic><topic>Peptides - analysis</topic><topic>Proteomics - methods</topic><topic>Reference Standards</topic><topic>Reproducibility of Results</topic><topic>RP HPLC</topic><topic>Shotgun proteomics</topic><topic>Software</topic><topic>Tandem Mass Spectrometry - methods</topic><topic>Technology</topic><topic>Time Factors</topic><topic>Trypsin - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>McQueen, Peter</creatorcontrib><creatorcontrib>Spicer, Vic</creatorcontrib><creatorcontrib>Rydzak, Thomas</creatorcontrib><creatorcontrib>Sparling, Richard</creatorcontrib><creatorcontrib>Levin, David</creatorcontrib><creatorcontrib>Wilkins, John A.</creatorcontrib><creatorcontrib>Krokhin, Oleg</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environmental Sciences and Pollution Management</collection><jtitle>Proteomics (Weinheim)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>McQueen, Peter</au><au>Spicer, Vic</au><au>Rydzak, Thomas</au><au>Sparling, Richard</au><au>Levin, David</au><au>Wilkins, John A.</au><au>Krokhin, Oleg</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: Case study using a whole cell digest of Clostridium thermocellum</atitle><jtitle>Proteomics (Weinheim)</jtitle><addtitle>Proteomics</addtitle><date>2012-04</date><risdate>2012</risdate><volume>12</volume><issue>8</issue><spage>1160</spage><epage>1169</epage><pages>1160-1169</pages><issn>1615-9853</issn><eissn>1615-9861</eissn><abstract>We have developed a real‐time graphic‐processor‐unit‐based search engine capable of high‐quality peptide identifications in <500 μs per spectrum. The steps of peptide/protein identification, in‐silico prediction of all possible tryptic peptides from these proteins, and the prediction of their expected retention times and m/z values take less than 5 s per cycle over ∼3000 MS/MS spectra. This lays the foundation for information‐dependent acquisition with exclusion lists generated on‐the‐fly, as the instrument continues to acquire data. While a complete evaluation of the dynamic exclusion system requires the participation from instrument vendors, we conducted a series of model experiments using a whole cell tryptic digestion of the bacterium Clostridium thermocellum. We ran a series of five iterative LC‐MS/MS runs, adding a new exclusion list at each of four chromatographic “tripping points” – the elution times of the four standard peptides spiked into the sample. Retention times of these standard peptides were also used for real‐time “chromatographic calibration.” The dynamic exclusion approach gave a ∼5% increase in confident protein identification (for typical 2 h LC‐MS/MS run), and reduced the average number of identified peptides per protein from 4.7 to 2.9. Its application to a two‐times shorter gradient gave a ∼17% increase in proteins identified. Further improvements are possible for instruments with better mass accuracy, by employing a more accurate retention prediction algorithm and by developing better understanding of the possible chemical modifications and fragmentations produced during electrospray ionization.</abstract><cop>Germany</cop><pub>Blackwell Publishing Ltd</pub><pmid>22577018</pmid><doi>10.1002/pmic.201100425</doi><tpages>10</tpages></addata></record> |
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| identifier | ISSN: 1615-9853 |
| ispartof | Proteomics (Weinheim), 2012-04, Vol.12 (8), p.1160-1169 |
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| subjects | Algorithms Automatic Data Processing Chromatography, Liquid - methods Clostridium thermocellum Clostridium thermocellum - chemistry Information-dependent acquisition Peptide retention prediction Peptides - analysis Proteomics - methods Reference Standards Reproducibility of Results RP HPLC Shotgun proteomics Software Tandem Mass Spectrometry - methods Technology Time Factors Trypsin - chemistry |
| title | Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: Case study using a whole cell digest of Clostridium thermocellum |
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