A comparison of the accuracy of iTRAQ quantification by nLC-ESI MSMS and nLC-MALDI MSMS methods
The accuracy of quantification obtained using the iTRAQ labelling methodology for measuring protein ratios more extreme than 1:1 was investigated. A comparison of nLC-ESI MSMS and nLC-MALDI MSMS analysis routes was performed. A fixed concentration of a standard six protein mix was spiked with two pr...
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| Veröffentlicht in: | Journal of proteomics 2010-05, Vol.73 (7), p.1391-1403 |
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| container_title | Journal of proteomics |
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| creator | Shirran, Sally L. Botting, Catherine H. |
| description | The accuracy of quantification obtained using the iTRAQ labelling methodology for measuring protein ratios more extreme than 1:1 was investigated. A comparison of nLC-ESI MSMS and nLC-MALDI MSMS analysis routes was performed. A fixed concentration of a standard six protein mix was spiked with two proteins at a range of concentrations. The two data analysis programmes, Mascot and ProteinPilot Paragon, were also compared. Whilst the lower ratios could be measured accurately, greater discrepancies were seen for the higher ratios, particularly by nLC-ESI MSMS. Filtering out the weaker reporter ion signals improved the accuracy of the ratios: this is likely due to several factors which are explored in more detail. Overall, analysis by nLC-MALDI MSMS followed by Mascot interpretation gave the most accurate results.
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| doi_str_mv | 10.1016/j.jprot.2010.03.003 |
| format | Article |
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[Display omitted]</description><subject>Biological and medical sciences</subject><subject>Diverse techniques</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Profiling - methods</subject><subject>iTRAQ quantification</subject><subject>Mascot</subject><subject>Molecular and cellular biology</subject><subject>nLC-ESI MSMS</subject><subject>nLC-MALDI MSMS</subject><subject>Peptide Mapping - methods</subject><subject>ProteinPilot</subject><subject>Reproducibility of Results</subject><subject>Sensitivity and Specificity</subject><subject>Spectrometry, Mass, Electrospray Ionization - methods</subject><subject>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods</subject><issn>1874-3919</issn><issn>1876-7737</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kE9vEzEQxS0EoiXwCZDQXjhuGK-z6_UBpCgUqJSoKsndcsZj4ihZB3tTKd8e5w-lvXDy-Pm9N9aPsfcchhx482k9XO9i6IcVZAXEEEC8YNe8lU0ppZAvT_OoFIqrK_YmpTVAw6WSr9lVBZUAVdXXTI8LDNudiT6Frgiu6FdUGMR9NHg43v3i5_i--L03Xe-dR9P77Fseim46KW_mt8VsPpsXprMnYTaefr1IW-pXwaa37JUzm0TvLueALb7dLCY_yund99vJeFpiXY_6ctTQ0hlqnHSglDVScGzyvGyUqpyDmiS10lohnWzIErTIhXAIFVItnRiwL-fa3X65JYvU9dFs9C76rYkHHYzXz186v9K_woOu2hakGuUCcS7AGFKK5B6zHPQRt17rE259xK1B6Iw7pz48XfuY-cs3Gz5eDCah2bhoOvTpn6-SNVe5acA-n32UGT14ijqhpw7J-kjYaxv8fz_yB7ffn08</recordid><startdate>20100507</startdate><enddate>20100507</enddate><creator>Shirran, Sally L.</creator><creator>Botting, Catherine H.</creator><general>Elsevier B.V</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>IQODW</scope><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>5PM</scope></search><sort><creationdate>20100507</creationdate><title>A comparison of the accuracy of iTRAQ quantification by nLC-ESI MSMS and nLC-MALDI MSMS methods</title><author>Shirran, Sally L. ; Botting, Catherine H.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c554t-46ebfae6f7f099da731c67f0b6992ff05e7e87dd37f76ede08c133fc02ce57f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Biological and medical sciences</topic><topic>Diverse techniques</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Profiling - methods</topic><topic>iTRAQ quantification</topic><topic>Mascot</topic><topic>Molecular and cellular biology</topic><topic>nLC-ESI MSMS</topic><topic>nLC-MALDI MSMS</topic><topic>Peptide Mapping - methods</topic><topic>ProteinPilot</topic><topic>Reproducibility of Results</topic><topic>Sensitivity and Specificity</topic><topic>Spectrometry, Mass, Electrospray Ionization - methods</topic><topic>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shirran, Sally L.</creatorcontrib><creatorcontrib>Botting, Catherine H.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of proteomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shirran, Sally L.</au><au>Botting, Catherine H.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A comparison of the accuracy of iTRAQ quantification by nLC-ESI MSMS and nLC-MALDI MSMS methods</atitle><jtitle>Journal of proteomics</jtitle><addtitle>J Proteomics</addtitle><date>2010-05-07</date><risdate>2010</risdate><volume>73</volume><issue>7</issue><spage>1391</spage><epage>1403</epage><pages>1391-1403</pages><issn>1874-3919</issn><eissn>1876-7737</eissn><abstract>The accuracy of quantification obtained using the iTRAQ labelling methodology for measuring protein ratios more extreme than 1:1 was investigated. A comparison of nLC-ESI MSMS and nLC-MALDI MSMS analysis routes was performed. A fixed concentration of a standard six protein mix was spiked with two proteins at a range of concentrations. The two data analysis programmes, Mascot and ProteinPilot Paragon, were also compared. Whilst the lower ratios could be measured accurately, greater discrepancies were seen for the higher ratios, particularly by nLC-ESI MSMS. Filtering out the weaker reporter ion signals improved the accuracy of the ratios: this is likely due to several factors which are explored in more detail. Overall, analysis by nLC-MALDI MSMS followed by Mascot interpretation gave the most accurate results.
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| identifier | ISSN: 1874-3919 |
| ispartof | Journal of proteomics, 2010-05, Vol.73 (7), p.1391-1403 |
| issn | 1874-3919 1876-7737 |
| language | eng |
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| source | MEDLINE; ScienceDirect Journals (5 years ago - present) |
| subjects | Biological and medical sciences Diverse techniques Fundamental and applied biological sciences. Psychology Gene Expression Profiling - methods iTRAQ quantification Mascot Molecular and cellular biology nLC-ESI MSMS nLC-MALDI MSMS Peptide Mapping - methods ProteinPilot Reproducibility of Results Sensitivity and Specificity Spectrometry, Mass, Electrospray Ionization - methods Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods |
| title | A comparison of the accuracy of iTRAQ quantification by nLC-ESI MSMS and nLC-MALDI MSMS methods |
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