Table 5.

Quantification results of the sample 1:3 mix.

Protein Id	Protein name	Quant						EE	Pro Quant™			Bias
								2,9929				2,8491
		Ratio	n	IQR	RMS	LSE	μ	σ	Ratio	n	pVal	EF
P00722	Beta-galactosidase BGAL_ECOLI	1.0072	100	0.1606	0.0287	1.0550	0.0323	0.1952	0.9862	100	0.3045	1.0268
P00698	Lysozyme C precursor LYSC_CHICK	1.0545	47	0.1971	0.0202	1.0891	0.0757	0.1392	1.0088	47	0.6644	1.0410
P02787	Serotransferrin precursor TRFE_HUMAN	1.0005	124	0.1832	0.0213	1.0363	0.0144	0.1973	1.0261	124	0.0536	1.0264
P02769	Serum albumin precursor ALBU_BOVIN	1.0305	64	0.1975	0.0331	1.0929	0.0624	0.2183	1.0329	64	0.0099	1.0245
P00711	Alpha-lactalbumin precursor LALBA_BOVIN	0.9618	8	0.1667	0.0083	0.9546	-0.0511	0.1022	1.0194	8	0.5019	1.0601
P02754	Beta-lactoglobulin precursor (LACB_BOVIN)	1.0366	54	0.1569	0.0099	1.0436	0.0331	0.1388	0.9839	54	0.4429	1.0434

The quantification results of the sample 1:3 mix are shown that include all peptides of each identified protein. Listed are the Protein Id, the protein name, the protein ratio (ratio) with the experiment error (EE) and the bias estimate of Quant and ProQuant™, respectively. The number of MS/MS spectra is listed in column n. Furthermore, several quality factors calculated by Quant are shown: the least squares estimator (LSE), interquartile range (IQR), root-mean-square value (RMS), mean value (μ) and standard deviation (σ). μ and σ were calculated from the log-transformed data. The results of ProQuant™ are taken from the ProGroup™ output that yields a p-value (pVal) and an error factor (EF) as described previously [35]. The experiment error of Quant (bias of ProQuant™) indicates the overall protein mixing ratio. The protein ratio results are normalized by this factor.