Table 2.

Summary of results obtained for mixture of standard proteins using the integrated approach. Tentative identifications of proteins and modified proteins were accomplished by matching bottom-up data with the measured intact protein masses. Protein assignments (with exception of α-caseins) were subsequently confirmed by protein MS/MS analyses using collected fractions.

Spot in Fig 2B	Measured Mr (Da)	Theoretical Mr (Da)	Protein	Modifications	Eluted in Fractions	MMA (ppm)
1	29024.7313	29024.7312	carbonic anhydrase II	Removal of N-term Met, N-acetylation	[33,36]	0.00
2	18363.4561	18363.4538	β-lactoglobulin A	2 disulfide bonds	[35,37]	0.13
3	18276.4323	18276.4169	β-lactoglobulin B	2 disulfide bonds	[32,34]	0.84
4	18097.4866	18097.471	Calmodulin	with His-tag	[31.33]	0.86
5	16950.9857	16950.992	myoglobin	Intact protein	[34,36]	−0.37
6	16993.0104	16993.0025	myoglobin	Lys-acetylation	42	0.46
7	24092.3436	24092.2661	β-casein, variant B	5 phosphorylations, P67H(SNP) and S122R (SNP) to variant A2	26	3.22
8	24023.2204	24023.1971	β-casein, variant A1	5 phosphorylations, P67H(SNP) to variant A2	27	0.97
9	23983.2346	23983.191	β-casein, variant A2	5 phosphorylations	[28,30]	1.82
10	12229.2211	12229.2193	cytochrome C	Removal of N-term Met, N-acetylation, with Heme	[3,12]	0.15
11	8564.6471	8564.6302	ubiquitin	Intact protein	[4,7]	1.97
12	25226.9975	25227.0194	α-casein2	11 phosphorylations	14	0.87
13	25306.1167	25305.9875	α-casein2	12 phosphorylations	14	−5.18