Table 2.

Np-RP HPLC MALDI-TOF MS versus SDS-PAGE/MALDI-TOF MS PMF results comparison.

			MW (Da)(ii)		In-gel digestion		In-well digestion
(i)ID	Protein	SwissProt Id. #	Theor.	Obs.	# peptides matched	Coverage (%)	# peptides matched	Coverage (%)
A	Insulin	P01317	5733	5740	1	(iii)	2	(iii)
B	Cytochrome C	P62894	11572	11741	14	66	11	57
C	Trypsin Inhibitor	P01071	20041	19432	8	33	10	37
D	GAPDH tetramer	P46406	35689 146 KDa	34371	11	30	9	24
E	Myoglobin	P68082	16951	16379	16	81	16	94
F	Catalase tetramer	P00432	59784 200 kDa	56953	24	40	21	37
G	β-Lactoglobulin dimmer	P02754	18281 36 kDa	17778	9	48	9	56
H	Glucose oxidase dimmer	P13006	63273 160 kDa	Nd	10	22	11	30
I	Ferritin (LC) multimer	P02791	19819 450 kDa	Nd	(iv)	(iv)	7	39 (v)

The protein standard (1 µg of each protein) was separated by either np-RP HPLC or by SDS-PAGE electrophoresis. Corresponding fractions or bands were respectively in-well or in-gel digested with trypsin and resulting peptides were analyzed by MALDI-TOF MS. For samples obtained from np-RP HPLC intact MALDI-TOF MS spectra were analyzed and corresponding molecular weights measured. The list of the peaks corresponding to each spectrum was submitted to Mascot database search software for protein identification. The number of peptides matching and percentage of sequence coverage were determined.

⁽ⁱ⁾Protein ID and intact mass values correspond to Figure 1 and Figure 3a, PMF information is from Figure 3b.

⁽ⁱⁱ⁾Molecular weights were obtained from the UniProt Knowledgebase (ca.expasy.org); masses of multimeric forms are estimated.

⁽ⁱⁱⁱ⁾Because insulin possesses only two sites of trypsin cleavage, the percentage of coverage was not informative enough to be shown.

^(iv)Ferritin (500 kDa), which is composed of 24 peptide chains was not detected on the gel, probably due to the presence of reducing agent in the sample buffer.

^(v)The percentage of sequence coverage of the in-well digestion is given for Ferritin light chain (20 kDa).