LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise

Table 1 Performance comparison of preprocessing methods.

Protein concentration		2.5 fmol	5 fmol	7.5 fmol	10 fmol	25 fmol	50 fmol
LIMPIC	Average intensity	1.17	4.65	5.32	17.07	94.03	277.37
	Standard deviation	0.10	0.39	0.61	2.70	14.01	42.48
	Coefficient of variation	0.09	0.08	0.12	0.16	0.15	0.15
APEX & CENTROID	Average intensity	1.31	5.36	6.05	14.94	88.48	283.08
	Standard deviation	0.32	0.74	0.97	2.40	12.76	42.48
	Coefficient of variation	0.24	0.14	0.16	0.16>	0.14	0.15
CROMWELL	Average intensity	0	0	4.01	12.76	85.34	275.50
	Standard deviation	0	0	1.52	2.95	13.79	48.49
	Coefficient of variation	-	-	0.38	0.23	0.16	0.17

LIMPIC, APEX, CENTROID and CROMWELL preprocessing methods were evaluated from in-vitro protein spectra at different dilutions of cytochrome C. For each method, the average peak intensity, the standard deviation and the coefficient of variation are provided. The underlined values were manually obtained from the mass spectra, because the peak-picking algorithms did not allow to detect the peak.