Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: Non-label methods comparison, q-values and LOWESS curve fitting
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| Title: | Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: Non-label methods comparison, q-values and LOWESS curve fitting |
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| Authors: | Xia, Qiangwei1,2, Wang, Tiansong1,2, Park, Yoonsuk3, Lamont, Richard J.3, Hackett, Murray1 mhackett@u.washington.edu |
| Source: | International Journal of Mass Spectrometry. Jan2007, Vol. 259 Issue 1-3, p105-116. 12p. |
| Subjects: | Proteomics, Porphyromonas gingivalis, Mass spectrometry, Spectrometers |
| Abstract: | Abstract: Differential analysis of whole cell proteomes by mass spectrometry has largely been applied using various forms of stable isotope labeling. While metabolic stable isotope labeling has been the method of choice, it is often not possible to apply such an approach. Four different label free ways of calculating expression ratios in a classic “two-state” experiment are compared: signal intensity at the peptide level, signal intensity at the protein level, spectral counting at the peptide level, and spectral counting at the protein level. The quantitative data were mined from a dataset of 1245 qualitatively identified proteins, about 56% of the protein encoding open reading frames from Porphyromonas gingivalis, a Gram-negative intracellular pathogen being studied under extracellular and intracellular conditions. Two different control populations were compared against P. gingivalis internalized within a model human target cell line. The q-value statistic, a measure of false discovery rate previously applied to transcription microarrays, was applied to proteomics data. For spectral counting, the most logically consistent estimate of random error came from applying the locally weighted scatter plot smoothing procedure (LOWESS) to the most extreme ratios generated from a control technical replicate, thus setting upper and lower bounds for the region of experimentally observed random error. [Copyright &y& Elsevier] |
| Copyright of International Journal of Mass Spectrometry is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 23052346 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: Non-label methods comparison, q-values and LOWESS curve fitting – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Xia%2C+Qiangwei%22">Xia, Qiangwei</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Wang%2C+Tiansong%22">Wang, Tiansong</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Park%2C+Yoonsuk%22">Park, Yoonsuk</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Lamont%2C+Richard+J%2E%22">Lamont, Richard J.</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Hackett%2C+Murray%22">Hackett, Murray</searchLink><relatesTo>1</relatesTo><i> mhackett@u.washington.edu</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22International+Journal+of+Mass+Spectrometry%22">International Journal of Mass Spectrometry</searchLink>. Jan2007, Vol. 259 Issue 1-3, p105-116. 12p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Proteomics%22">Proteomics</searchLink><br /><searchLink fieldCode="DE" term="%22Porphyromonas+gingivalis%22">Porphyromonas gingivalis</searchLink><br /><searchLink fieldCode="DE" term="%22Mass+spectrometry%22">Mass spectrometry</searchLink><br /><searchLink fieldCode="DE" term="%22Spectrometers%22">Spectrometers</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Abstract: Differential analysis of whole cell proteomes by mass spectrometry has largely been applied using various forms of stable isotope labeling. While metabolic stable isotope labeling has been the method of choice, it is often not possible to apply such an approach. Four different label free ways of calculating expression ratios in a classic “two-state” experiment are compared: signal intensity at the peptide level, signal intensity at the protein level, spectral counting at the peptide level, and spectral counting at the protein level. The quantitative data were mined from a dataset of 1245 qualitatively identified proteins, about 56% of the protein encoding open reading frames from Porphyromonas gingivalis, a Gram-negative intracellular pathogen being studied under extracellular and intracellular conditions. Two different control populations were compared against P. gingivalis internalized within a model human target cell line. The q-value statistic, a measure of false discovery rate previously applied to transcription microarrays, was applied to proteomics data. For spectral counting, the most logically consistent estimate of random error came from applying the locally weighted scatter plot smoothing procedure (LOWESS) to the most extreme ratios generated from a control technical replicate, thus setting upper and lower bounds for the region of experimentally observed random error. [Copyright &y& Elsevier] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of International Journal of Mass Spectrometry is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1016/j.ijms.2006.08.004 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 12 StartPage: 105 Subjects: – SubjectFull: Proteomics Type: general – SubjectFull: Porphyromonas gingivalis Type: general – SubjectFull: Mass spectrometry Type: general – SubjectFull: Spectrometers Type: general Titles: – TitleFull: Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: Non-label methods comparison, q-values and LOWESS curve fitting Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Xia, Qiangwei – PersonEntity: Name: NameFull: Wang, Tiansong – PersonEntity: Name: NameFull: Park, Yoonsuk – PersonEntity: Name: NameFull: Lamont, Richard J. – PersonEntity: Name: NameFull: Hackett, Murray IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Text: Jan2007 Type: published Y: 2007 Identifiers: – Type: issn-print Value: 13873806 Numbering: – Type: volume Value: 259 – Type: issue Value: 1-3 Titles: – TitleFull: International Journal of Mass Spectrometry Type: main |
| ResultId | 1 |
