Comparative proteomics: assessment of biological variability and dataset comparability

BMC Bioinformatics

Table 2 Relative amount of GFP between high and low expression system at different stage of cell growth

Samples	Comparison ^a	R _TS	Internal standard ^b	Relative amount of GFP
				LC-MS/MS ^c	FL ^d
High-1 vs Low-1	1A/3A	1.34	−1.43 ± 0.44	2.49 ± 0.57	2.86 ± 0.42
	1B/3A	1.12	−1.03 ± 0.32	2.66 ± 0.71
	1C/3A	1.29	−1.07 ± 0.38	2.51 ± 0.75
	1A/3B	1.05	−1.23 ± 0.66	3.88 ± 1.69
	1B/3B	1.14	1.23 ± 0.53	2.12 ± 0.66
	1C/3B	1.65	1.22 ± 0.77	2.06 ± 0.94
	1A/3C	1.88	−1.44 ± 0.87	7.09 ± 3.17
	1B/3C	1.57	−1.01 ± 0.51	3.89 ± 1.23
	1C/3C	1.09	1.35 ± 0.44	3.48 ± 0.59
High-2 vs Low-2	2A/4A	1.18	−1.09 ± 0.27	3.27 ± 0.70	4.00 ± 0.62
	2B/4A	1.14	−1.12 ± 0.37	3.66 ± 1.08
	2C/4A	1.14	−1.14 ± 0.34	4.00 ± 1.09
	2A/4B	1.04	−1.04 ± 0.19	3.87 ± 0.61
	2B/4B	1.01	−1.06 ± 0.20	4.28 ± 0.76
	2C/4B	1.00	−1.09 ± 0.27	4.73 ± 1.10
	2A/4C	1.05	−1.06 ± 0.23	3.80 ± 0.79
	2B/4C	1.02	−1.08 ± 0.30	4.24 ± 1.06
	2C/4C	1.02	−1.05 ± 0.19	4.58 ± 0.89

^aNumber indicates the group of sample and A, B, and C indicates the biological replicates as described in Table 1.
^bInternal standard is the average relative amount of internal standards between two biological replicates.
^cThe relative amount of GFP between two biological replicates of samples calculated by the spectral counting method with the use of internal standards.
^dFluorescence was measured in triplicate from separate biological replicates.

ISSN: 1471-2105