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Table 5 Proteins associated with glioma vessel formation established from enzymatic digested by trypsin peptide masses that are exclusively present in the "glioma vessels" group.

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

Measured mass MH+ (Da)

Calculated mass MH+ (Da)

ppm

p-value Intensity H against S

Intensity H > S

Glioma vessels (H)

Normal vessels (S)

Glioma tissue(TH)

Normal tissue (TS)

SwissProt TM accession code Q9UKI2, name: Cdc42 effector protein 3 (Binder of Rho GTPases 2)

1229.6644

1229.66365

0.61

0.00411

yes

6

0

0

0

1656.8022

1656.80295

0.45

0.13120

yes

5

1&

0

0

1620.7609

1620.76073

0.10

0.25509

yes

4

0

0

0

1772.8870

1772.88871

0.96

0.80459

no

3

3

1

1

SwissProt TM accession code, name: Fibronectin precursor (FN) (Cold-insoluble globulin) (CIG)

1807.9063

1807.90469

0.89

0.00089

yes

8

0

0

0

1355.6954

1355.69536

0.03

0.00125

yes

7

0

0

0

1625.8539

1625.85196

1.19

0.00232

yes

5

0

0

0

1349.6848*

1349.68481

0.01

0.00345

yes

7

0

0

0

1926.0516

1926.04832

1.70

0.00503

yes

8

1&

0

0

1629.8728*

1629.87067

1.31

0.00873

yes

5

0

0

0

2470.3200

2470.31874

0.51

0.01233

yes

7

1

1

0

1078.5537

1078.55275

0.88

0.01835

no

0

3

1

1

1818.9739

1818.97078

1.72

0.02049

yes

5

0

0

0

2524.3649

2524.36568

0.31

0.02049

yes

5

0

0

0

1401.6649*

1401.66580

0.64

0.02170

yes

6

0

0

0

1341.6739

1341.67570

1.34

0.02663

yes

5

1

3

0

1110.5413

1110.54257

1.14

0.06243

yes

4

0

2

0

1593.8126

1593.81186

0.46

0.06243

yes

6

1

1

0

1292.6740

1292.67324

0.59

0.06373

yes

5

1

0

1

1297.7117

1297.71102

0.52

0.09473

yes

3

0

1

1

1591.8091

1591.80744

1.04

0.12668

yes

4

0

2

0

1235.5266

1235.52620

0.32

0.13120

yes

3

1

0

1

1431.7507

1431.74915

1.08

0.18754

yes

5

2

0

0

2139.9619

2139.96514

1.51

0.45543

yes

5

1

6

0

858.4301

858.43157

1.71

0.95436

no

2

1

2

0

1291.7265

1291.72560

0.70

1.00000

yes

3

3

1

0

SwissProt TM accession code Q99653, name: Calcium-binding protein p22 (Calcium-binding protein CHP) (Calcineurin homologous protein)

960.5588

960.55850

0.31

0.02082

yes

6

0

4

0

1138.5646

1138.56262

1.74

0.00959

yes

5

0

0

1

1508.7103

1508.70876

1.02

0.05363

yes

5

0

0

0

SwissProt TM accession code P35579, name: Myosin-9 (Myosin heavy chain, non-muscle IIa)

1869.9677*

1869.96645

0.67

0.00170

yes

6

0

0

0

1155.6643

1155.66325

0.91

0.00310

yes

5

0

0

0

1949.9955

1949.99268

1.45

0.01285

yes

8

0

0

0

2493.1740*

2493.17392

0.03

0.04085

yes

6

0

0

0

2472.1699

2472.17356

1.48

0.05363

yes

5

0

0

0

1393.7099#

1393.71102

0.80

0.07335

no

1

4

3

7

1946.0059

1946.00765

0.90

0.33559

yes

7

4

6

0

924.4946

924.49377

0.90

0.60387

yes

3

2

3

0

1309.6023†

1309.60188

0.32

0.61715

yes

4

3

1

0

1193.6166*

1193.61606

0.45

0.75200

yes

3

2

4

2

1310.7038$

1310.70626

1.88

1.00000

yes

1

0

7

0

  1. The listed proteins are found by a MASCOT™ search with 2 or more hits between measured and calculated tryptic peptide masses with an error tolerance of 2 ppm. Only proteins are listed that had at least one peptide mass with a Wilcoxon-Mann-Whitney p-value < 0.01 comparing the peak intensities of glioma vessels with normal vessels.
  2. * WARP-LC MS-MS MALDI-TOF glioma tissue and vessels (see Additional file 1).
  3. # SwissProtTM accession code: P40925, name: Malate dehydrogenase, cytoplasmic, identified by WARP-LC MS-MS on glioma tissue and vessels and normal tissue and vessels (see Additional file 1).
  4. † SwissProtTM accession code: P08670, name: Vimentin, sequence: NLQEAEEWYK, MALDI TOF MS-MS by hand on the “glioma tissue and vessels” LC-MALDI plate using the BiotoolsTM 3.0 (build 1.68) software.
  5. $ SwissProtTM accession code: P62805, name: Histone H4, identified by WARP-LC MS-MS on glioma tissue and vessels and normal tissue and vessels (see Additional file 1).
  6. & outlier sample S10.
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BMC Bioinformatics

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