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

doi:10.1186/1471-2105-10-43

BMC Bioinformatics

Volume 10

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Methodology article

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

Qingbo Li¹^,2 and Bryan AP Roxas¹

¹Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA

²Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA

author email corresponding author email

BMC Bioinformatics 2009, 10:43doi:10.1186/1471-2105-10-43


Published:	2 February 2009

Additional files

Additional File 1:

Table S1. List of the PCS abundance ratios of the sample pair S_P/R_Pfor the 1709 detected PCSs. The abundance ratios were calculated for the UL and IS PCSs separately. These ratios were also calculated for each of the four permuted sample-pairings.

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Additional File 2:

Table S2. The 349 detected proteins are listed in the worksheet 'Protein List'. Shown to the right of the protein locus names are the protein relative abundances, the p-values and the results of the t-test and the Wilcoxon ranksum test for the four permuted sample-pairings of the sample pair S_P/R_P. 'mean' is the average PCS abundance ratio of a protein. 't-test' indicates the result of the t-test (p < 0.05). 'ranksum test' indicates the result of the Wilcoxon ranksum test (p < 0.05). The p-values of these two tests are also shown. The worksheet 'FDR' contains the formula to calculate a FDR with the values in the 'Protein List' worksheet. The three values in the green cells can be interactively changed to observe the response of the FDR and the numbers of positives and false positives. The 'FDR' worksheet is reminiscent of Table 1.

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Additional File 3:

Table S3. Validation with different combinations among S_P, R_P, S_A, S_B, and S_C.

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Additional File 4:

Table S4. Validation by comparing the results in this study with those in a previous study [6].

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