MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments
<p>Abstract</p> <p>Background</p> <p>Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, se...
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| Format: | Article |
| Language: | English |
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BMC
2011-03-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/12/74 |
| _version_ | 1811276528883859456 |
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| author | Haskins William E Petritis Konstantinos Zhang Jianqiu |
| author_facet | Haskins William E Petritis Konstantinos Zhang Jianqiu |
| author_sort | Haskins William E |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides on time-of-flight (TOF) instruments: LC peak boundary detection, thermal noise suppression, interference removal and mass drift correction. We propose to use the Maximum Ratio Combining (MRC) method to extract MS signal templates for interference detection/removal and LC peak boundary detection. In our method, MRCQuant, MS templates are extracted directly from experimental values, and the mass drift in each LC-MS run is automatically captured and compensated. We compared the quantification accuracy of MRCQuant to that of another representative LC-MS quantification algorithm (msInspect) using datasets downloaded from a public data repository.</p> <p>Results</p> <p>MRCQuant showed significant improvement in the number of accurately quantified peptides.</p> <p>Conclusions</p> <p>MRCQuant effectively addresses major issues in the relative quantification of LC-MS-based proteomics data, and it provides improved performance in the quantification of low abundance peptides.</p> |
| first_indexed | 2024-04-12T23:58:06Z |
| format | Article |
| id | doaj.art-998e80a31d3642bd9cb0ab404bdb2568 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-12T23:58:06Z |
| publishDate | 2011-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-998e80a31d3642bd9cb0ab404bdb25682022-12-22T03:11:25ZengBMCBMC Bioinformatics1471-21052011-03-011217410.1186/1471-2105-12-74MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instrumentsHaskins William EPetritis KonstantinosZhang Jianqiu<p>Abstract</p> <p>Background</p> <p>Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides on time-of-flight (TOF) instruments: LC peak boundary detection, thermal noise suppression, interference removal and mass drift correction. We propose to use the Maximum Ratio Combining (MRC) method to extract MS signal templates for interference detection/removal and LC peak boundary detection. In our method, MRCQuant, MS templates are extracted directly from experimental values, and the mass drift in each LC-MS run is automatically captured and compensated. We compared the quantification accuracy of MRCQuant to that of another representative LC-MS quantification algorithm (msInspect) using datasets downloaded from a public data repository.</p> <p>Results</p> <p>MRCQuant showed significant improvement in the number of accurately quantified peptides.</p> <p>Conclusions</p> <p>MRCQuant effectively addresses major issues in the relative quantification of LC-MS-based proteomics data, and it provides improved performance in the quantification of low abundance peptides.</p>http://www.biomedcentral.com/1471-2105/12/74 |
| spellingShingle | Haskins William E Petritis Konstantinos Zhang Jianqiu MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments BMC Bioinformatics |
| title | MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments |
| title_full | MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments |
| title_fullStr | MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments |
| title_full_unstemmed | MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments |
| title_short | MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments |
| title_sort | mrcquant an accurate lc ms relative isotopic quantification algorithm on tof instruments |
| url | http://www.biomedcentral.com/1471-2105/12/74 |
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