A simple and reliable protocol for mouse serum proteome profiling studies by use of two-dimensional electrophoresis and MALDI TOF/TOF mass spectrometry

Table 2 New proteins, spectra interpretation and validation

No	No Table 1	Swiss Prot entry	Swiss Prot accession	putative PTMs	Subcellular location	Mw (KDa)	pI	RMS error (ppm)	matrix	Swiss Prot	NCBInr	MSDB	Nr of matched peptides (Mascot)	Nr of matched peptides (Peptide Map)
1	16	ANGL6 MOUSE	Q8R0Z6	G	Secreted; highly expressed in the liver	51.4	9	38	DHB	56	58	55	4	3
2	17	ANXA2 MOUSE	P07356	P	Secreted, extracellular space, extracellular matrix, basement membrane. Melanosome	38.8	8	45	CHCA	82	81	82	5	3
3	25	C1R MOUSE	Q8CG16	G	Secreted	81.5	5	15	DHB CHCA	78	78	78	8	5
4	32	CS1A MOUSE	Q8CG14	G	Predominantly expressed in liver	78.3	5	11	DHB	66	66	66	6	5
5	72	LAC1 MOUSE	P01843		Secreted	11.7	6	4	DHB	70	70	70	4	3
6	74	ACTG MOUSE	P63260	P	Cytoplasm, cytoskeleton	42.1	5	28	DHB CHCA	188	188	188	16	15
7	76	CT160 MOUSE	Q8VCC6			22	10	35	CHCA	55	56	56	5	4
8	77	CUL1 MOUSE	Q9WTX6	G	Embryo fibroblasts and embryo preadipocytes	90.3	8	49	CHCA	62	62	62	7	6
9	81	K2C5 MOUSE	Q922U2	P	Expressed in epidermis	62	8	34	DHB	60	60	60	11	11
10	85	OST5 MOUSE	Q8BSL4	G	Golgi apparatus membrane; Single-pass type II membrane protein	40.7	10	35	CHCA	70	70	70	6	5
11	87	TPH1 MOUSE	P17532	P	Cytoplasmatic enzyme, pineal gland	51.9	6	30	CHCA	57	57	57	7	5
12	88	KPYM MOUSE	P52480	P	Liver, red cells, muscles, brain	58	7	39	DHB	53	53	53	11	10
13	89	DYN2 MOUSE	P39054	P	Cytoplasm	98	7	51	DHB CHCA	68	68	68	9	9

We listed here the 13 proteins which re not present in the previous mouse serum maps [6–9, 32, 33].
The SwissProt entries in Italic font are proteins not identified in mouse serum proteome so far [5–9, 32, 33]. RMS (Root Mean Square) error is the calculated error for set of matched mass values (in ppm) in Mascot Search (matrix science, LTD, UK). It is measured in ppm. RMS error defines the limit of peptide mass tolerance (Peptide tol +-) for Mascot Peptide Mass Fingerprint to obtain a significant score (p < 0.05) of matched peptides to select protein entry.
The results were first searched in SwissProt databank and furthermore in NCBInr and MSDB databanks. The same criteria were applied (such as: mus musculus for the taxonomy, < +/- 50 ppm as peptide tolerance and one missed cleavage allowed for trypsin enzyme). In bold we highlighted the significant score (p < 0.05) according to the chosen database (SwissProt >53, NCBInr and MSDB >61) [21, 51].
We also specified if one matrix or the combination of them allowed the identification.
Post translation modifications (PTMs). P: phosphorylation; G: Glycosylation.

ISSN: 1477-5956