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

<p>Abstract</p> <p>Background</p> <p>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 <it>Mycobacterium smegmatis </it>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 <it>t</it>-test.</p> <p>Results</p> <p>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 6 biological replicates. Each biological replicate was mixed with a common ¹⁵N-labeled reference culture cells for normalization prior to SDS/PAGE fractionation and LC/MS analysis. For each biological replicate, one center SDS/PAGE gel fraction was selected for triplicate LC/MS analysis. There were 121 proteins quantified in at least 5 of the 6 biological replicates. Of these 121 proteins, 106 were significant in differential expression by the <it>t</it>-test (<it>p </it>< 0.05) based on peptide-level replicates, 54 were significant in differential expression by SAM with Δ = 0.68 cutoff and false positive rate at 5%, and 29 were significant in differential expression by the <it>t</it>-test (<it>p </it>< 0.05) based on protein-level replicates. The results indicate that SAM appears to overcome the false positives one encounters using the peptide-based <it>t</it>-test while allowing for identification of a greater number of differentially expressed proteins than the protein-based <it>t</it>-test.</p> <p>Conclusion</p> <p>We demonstrate that the SAM method can be adapted for effective significance analysis of proteomic data. It provides much richer information about the protein differential expression profiles and is particularly useful in the estimation of false discovery rates and miss rates.</p

An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters

Abstract Background Many studies have provided algorithms or methods to assess a statistical significance in quantitative proteomics when multiple replicates for a protein sample and a LC/MS analysis are available. But, confidence is still lacking in using datasets for a biological interpretation without protein sample replicates. Although a fold-change is a conventional threshold that can be used when there are no sample replicates, it does not provide an assessment of statistical significance such as a false discovery rate (FDR) which is an important indicator of the reliability to identify differentially expressed proteins. In this work, we investigate whether differentially expressed proteins can be detected with a statistical significance from a pair of unlabeled protein samples without replicates and with only duplicate LC/MS injections per sample. A FDR is used to gauge the statistical significance of the differentially expressed proteins. Results We have experimented to operate on several parameters to control a FDR, including a fold-change, a statistical test, and a minimum number of permuted significant pairings. Although none of these parameters alone gives a satisfactory control of a FDR, we find that a combination of these parameters provides a very effective means to control a FDR without compromising the sensitivity. The results suggest that it is possible to perform a significance analysis without protein sample replicates. Only duplicate LC/MS injections per sample are needed. We illustrate that differentially expressed proteins can be detected with a FDR between 0 and 15% at a positive rate of 4–16%. The method is evaluated for its sensitivity and specificity by a ROC analysis, and is further validated with a [15N]-labeled internal-standard protein sample and additional unlabeled protein sample replicates. Conclusion We demonstrate that a statistical significance can be inferred without protein sample replicates in label-free quantitative proteomics. The approach described in this study would be useful in many exploratory experiments where a sample amount or instrument time is limited. Naturally, this method is also suitable for proteomics experiments where multiple sample replicates are available. It is simple, and is complementary to other more sophisticated algorithms that are not designed for dealing with a small number of sample replicates.</p