Significance analysis of microarray for relative quantitation of LC/MS data in proteomics.

BMC Bioinformatics
Bryan A P Roxas, Qingbo Li

Abstract

Although fold change is a commonly used criterion in quantitative proteomics for differentiating regulated proteins, it does not provide an estimation of false positive and false negative rates that is often desirable in a large-scale quantitative proteomic analysis. We explore the possibility of applying the Significance Analysis of Microarray (SAM) method (PNAS 98:5116-5121) to a differential proteomics problem of two samples with replicates. The quantitative proteomic analysis was carried out with nanoliquid chromatography/linear iron trap-Fourier transform mass spectrometry. The biological sample model included two Mycobacterium smegmatis unlabeled cell cultures grown at pH 5 and pH 7. The objective was to compare the protein relative abundance between the two unlabeled cell cultures, with an emphasis on significance analysis of protein differential expression using the SAM method. Results using the SAM method are compared with those obtained by fold change and the conventional t-test. We have applied the SAM method to solve the two-sample significance analysis problem in liquid chromatography/mass spectrometry (LC/MS) based quantitative proteomics. We grew the pH5 and pH7 unlabelled cell cultures in triplicate resulting in...Continue Reading

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Citations

Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Vincent J DenefJillian F Banfield
Apr 14, 2012·Molecular & Cellular Proteomics : MCP·Annsofi SandbergJanne Lehtiö
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Jan 13, 2021·The Journal of Experimental Biology·Emmanuelle Pales Espinosa, Bassem Allam
Apr 3, 2018·Fish & Shellfish Immunology·Rachel HartmanBassem Allam

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Methods Mentioned

BETA
Protein Assay

Software Mentioned

SAM
Matlab
BioWorks
Excel TTEST
Significance Analysis of Microarray
Quoil
R

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