Table 2.

Proteomic and Statistical Data of Spots That Were Significantly Different in Abundance over the Course of Breast Tumorigenesis^a

master spot numberb	FCc	FCd	FDRe	proteinf	IDg	MASCOT no.h	MOWSEi	% cov.j	MWk	pIl
407	−1.23 (0.0024)		0.0008	Heat shock 70 kDa protein 4-like	O95757	gi|31541941	76	2%	95479	5.63
468	1.28 (0.00046)			Mitochondrial inner membrane protein	Q16891	gi|48145703	392	12%	84027	6.08
				Gelsolin isoform b	P06396	gi|38044288	246	5%	80876	5.58
				Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 precursor	O60568	gi|4505891	42	1%	85302	5.69
473	1.28 (0.00015)			Gelsolin isoform b	P06396	gi|38044288	216	7%	80876	5.58
474	1.34 (5.80 × 10−5)		0.047	Gelsolin isoform b	P06396	gi|38044288	308	7%	80876	5.58
592	−1.23 (0.018)		0.012	Heat shock 70 kDa protein 8 isoform 1	P11142	gi|5729877	493	20%	71082	5.37
				Lamin B1	P20700	gi|5031877	320	12%	66653	5.11
598	−1.32 (3.4 × 10−6)		4.00 × 10−8	Heat shock 70 kDa protein 8 isoform 1	P11142	gi|5729877	539	24%	71082	5.37
				V-type proton ATPase catalytic subunit A	P38606	gi|291868	177	7%	68677	5.35
604	−2.30 (4.30 × 10−7)		1.10 × 10−10	Keratin, type II cytoskeletal 1	P04264	gi|11935049	116	4%	66198	8.16
606	−1.29 (5.0 × 10−7)		9.00 × 10−8	Heat shock 70 kDa protein 8 isoform 1	P11142	gi|5729877	587	20%	71082	5.37
				Heat shock 70 kDa protein 1	P08107	gi|4529893	275	7%	70280	5.48
				Lamin B2	Q03252	gi|27436951	247	7%	67762	5.29
				V-type proton ATPase catalytic subunit A	P38606	gi|291868	101	3%	68677	5.35
615	−1.20 (2.1 × 10−6)		0.03	Heat shock 70 kDa protein 1	P08107	gi|4529892	628	23%	70267	5.48
				Plastin 3	P13797	gi|7549809	84	2%	71279	5.41
				Lamin B2	Q03252	gi|345758	66	1%	59079	5.87
651	−1.17 (0.016)		0.027	T-complex protein 1 isoform a	P17987	gi|57863257	101	4%	60819	5.80
749	1.22 (0.0017)			FK506-binding protein 5	Q13451	gi|1145816	38	2%	50859	5.80
753	−1.44 (4.30 × 10−7)	−1.30 (0.01)	1.10 × 10−10	Keratin, type II cytoskeletal 7	P08729	gi|67782365	482	23%	51411	5.42
754	−1.30 (5.00 × 10−7)		3.50 × 10−6	Keratin, type II cytoskeletal 8	P05787	gi|181573	511	22%	53529	5.52
				Keratin, type II cytoskeletal 7	P08729	gi|67782365	455	20%	51411	5.40
919	−1.32 (0.00047)	−1.24 (0.01)	6.90 × 10−8	Chain A, The 2.1 A Structure Of A Tumour Suppressing Serpin	P36952	gi|62738363	113	5%	42259	5.72
920	−1.29 (0.00015)	−1.27 (0.041)	2.10 × 10−7	Chain A, The 2.8 A Structure Of A Tumour Suppressing Serpin	P36952	gi|62738525	137	8%	43071	5.72
1028	−1.55 (2.30 × 10−5)	−1.43 (0.01)	1.30 × 10−8	60S acidic ribosomal protein P0	P05388	gi|4506667	88	5%	34423	5.71
1387	1.51 (0.0019)		.015	Stathmin 1 isoform b	P16949	gi|224451142	131	18%	19925	6.51

^aBold text indicates spots that contained only one protein.

^bMaster spot number assigned by Decyder.

^cFold change between SHMEC and THMEC 40 d. Numbers in parentheses correspond to false discovery rate corrected p-values from a Student’s t test. Only statistically significant data is displayed.

^dFold change between THMEC 40 d and THMEC 80 d. Numbers in parentheses correspond to false discovery rate corrected p-values from a Student’s t test. Only statistically significant data is displayed.

^eFalse discovery rate corrected p-values from a One-way ANOVA (SHMEC/THMEC40 d/THMEC80 d). Only statistically significant data is displayed.

^fProtein name.

^gSwiss-Prot ID.

^hThe “gi” accession numbuer obtained from MASCOT database.

ⁱMOWSE score obtained from MASCOT database.

^jPercent coverage of fragmented peptides vs total peptide length.

^kPredicted molecular weight in daltons.

^lPredicted isoelectric point (pI).