A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation

Table 4 Proteins significantly up-regulated in the "glioma vessels" group with respect to the "normal vessels" group.

Name	SwissProt™ acc. code	Nr. hits p-value< 0.01	Nr. hits p-value< 0.1	MS-MS glioma vessels	MS-MS glioma tissue and vessels	MS-MS normal vessels	MS-MS normal tissue and vessels
Vimentin	P08670	12	18	yes	yes	no	no
Glial fibrillary acidic protein (GFAP)	P14136	3	12	yes	yes	yes	yes
Serum albumin precursor	P02768	4	10	yes	yes	no	no
Annexin A5	P08758	2	5	no	yes	no	no
Actin, cytoplasmic 1 (Beta-actin)	P60709	0	12	yes	yes	yes	yes
Keratin, type I cytoskeletal 10	P13645	0	8	yes	no	yes	no
Actin, alpha cardiac (Alpha-cardiac actin)	P68032	0	7	no	yes	no	yes
Desmin	P17661	0	6	no	yes	no	no
Calcium-binding protein p22 (Calcium-binding protein CHP)	Q99653	0	3	no	no	no	no

A number of 95 (4%) of the measured peptide masses with Wilcoxon-Mann-Whitney p-values < 0.01 and raised intensities in the glioma vessel group are compared with calculated peptide masses from proteins in the SwissProt™ database using MASCOT™. A mass tolerance of 2 ppm is used. The MASCOT™ search is repeated with another number of 442 (19%) of peptide masses that have a p-value < 0.1 and with up-regulated intensities in the "glioma vessels" group. Only proteins are listed that have at least three hits of experimental measured peptide masses corresponding within 2 ppm with the calculated peptide masses of these proteins.

ISSN: 1471-2105