Integrated multi-level quality control for proteomic profiling studies using mass spectrometry

BMC Bioinformatics

Table 1 Abridged results of replicate analysis presented in web QC tool.

	2–4 kDa					4–6 kDa					6–8 kDa					8–10 kDa
Sample ID	TIC	Nm TIC	# pk	sum pk ints	% pk dif	TIC	Nm TIC	# pk	sum pk ints	% pk dif	TIC	Nm TIC	# pk	sum pk ints	% pk dif	TIC	Nm TIC	# pk	sum pk ints	% pk dif
3965	✓	✓	✓	✓	0	✓	✓	✓	✓	0	✓	✓	✓	✓	0	✓	✓	✓	✓	0
4000	✓	✓	✓	✓	39	✓	✓	✓	✓	3	✓	✓	✓	✓	13	✓	✓	✓	✓	33
4008	✗	✓	✗	✗	16	✗	✓	✗	✓	22	✓	✓	✗	✗	19	✗	✓	✗	✓	9
4021	✓	✓	✓	✓	21	✓	✓	✓	✓	0	✓	✓	✓	✓	0	✓	✓	✓	✓	0
4344	✓	✓	✓	✗	6	✗	✗	✗	✗	0	✗	✗	✗	✗	0	✗	✗	✗	✓	0

For each biological replicate (labelled by sample ID) the technical replicates are compared for various parameters in mass segments of the low mass range (2–4, 4–6, 6–8, 8–10 kDa out of full 2–10 kDa range). The first four of these parameters are the total ion current, the normalised total ion current, the total number of peaks (common and non-common peaks) and the total intensity of peaks. A tick in the columns for each of these parameters indicates that the coefficient of variation (CV) for that variable for these technical replicates is less than the 95% quantile of CVs calculated from all possible pairs of the QC samples. Conversely a cross indicates that they are greater than this empirical limit. The fifth parameter is presented numerically and is the percentage of peaks significantly different in the technical replicates based on an empirical significance test (derived similarly from QC samples). Results for all biological replicates are given in Table S2 [see Additional file 4].

ISSN: 1471-2105