ELECTROPHORESIS Supporting Information for Electrophoresis DOI 10.1002/elps.200700936 Qiaozhen Lu, Nivetha Murugesan, Jennifer A. Macdonald, Shiaw-Lin Wu, Joel S. Pachter and William S. Hancock Analysis of mouse brain microvascular endothelium using immuno-laser capture microdissection coupled to a hybrid LTQ-FT-MS proteomics platform ª 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.electrophoresis-journal.com Table A. List of total proteins identified in CD31 immunostained LCM Sample Protein name Peptide (Hits) Coverag MW Accession (%) # keratin complex 1, acidic, gene 14 [Mus musculus] 15 (15 0 0 0 0) 2.56E+01 52866.70 21489935 neurofilament, light polypeptide [Mus musculus] 4 (4 0 0 0 0) 6.10E+00 61507.96 39204499 actin, beta, cytoplasmic [Mus musculus] 21 (21 0 0 0 0) 3.36E+01 41736.51 6671509 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha 11 (11 0 0 0 0) 2.03E+01 59752.23 6680748 subunit, isoform 1 [Mus musculus] vesicle-associated membrane protein 2 [Mus musculus] 4 (4 0 0 0 0) 3.45E+01 12690.70 6678551 tubulin, beta 6 [Mus musculus] 1 (1 0 0 0 0) 4.00E+00 50090.05 27754056 actin-like [Mus musculus] 2 (2 0 0 0 0) 5.60E+00 43600.63 8850209 hemoglobin alpha 1 chain [Mus musculus] 3 (3 0 0 0 0) 2.39E+01 15085.06 6680175 keratinocyte associated protein 1 [Mus musculus] 23 (23 0 0 0 0) 1.22E+01 59740.13 29789317 ATP synthase, H+ transporting mitochondrial F1 complex, beta 18 (18 0 0 0 0) 4.03E+01 56300.11 31980648 subunit [Mus musculus] tyrosine 3-monooxygenase/tryptophan 5-monooxygenase 3 (3 0 0 0 0) 1.80E+01 27770.96 6756041 activation protein, zeta polypeptide [Mus musculus] RAB3A, member RAS oncogene family [Mus musculus] 1 (1 0 0 0 0) 7.30E+00 24969.72 6679593 Na+/K+ -ATPase alpha 3 subunit [Mus musculus] 5 (5 0 0 0 0) 6.10E+00 115967.90 21450321 ATP synthase, H+ transporting, mitochondrial F0 complex, 1 (1 0 0 0 0) 1.46E+01 11424.42 31980744 subunit G [Mus musculus] actin, alpha 2, smooth muscle, aorta [Mus musculus] 1 (1 0 0 0 0) 4.80E+00 42008.73 6671507 hemoglobin, beta adult major chain [Mus musculus] 5 (5 0 0 0 0) 3.54E+01 15747.95 31982300 keratin complex 2, basic, gene 1 [Mus musculus] 21 (21 0 0 0 0) 6.20E+00 65223.21 6678643 Golli-mbp isoform 1 [Mus musculus] 12 (12 0 0 0 0) 1.92E+01 27167.40 6754658 vacuolar H+ATPase B2 [Mus musculus] 1 (1 0 0 0 0) 2.90E+00 56550.50 19705578 Na+/K+ -ATPase beta 2 subunit [Mus musculus] 1 (1 0 0 0 0) 4.10E+00 33343.89 7242138 PREDICTED: similar to Keratin, type I cytoskeletal 10 27 (27 0 0 0 0) 8.70E+00 106713.90 94391959 (Cytokeratin-10) (CK-10) (Keratin-10) (K10) (56 kDa cytokeratin) (Keratin, type I cytoskeletal 59 kDa) [Mus musculus] tubulin, alpha 3 [Mus musculus] 8 (8 0 0 0 0) 1.67E+01 49959.23 6678465 tubulin, alpha 4 [Mus musculus] 1 (1 0 0 0 0) 3.30E+00 49924.10 6678467 tubulin, beta 2 [Mus musculus] 7 (7 0 0 0 0) 9.20E+00 49906.66 33859488 keratin complex 2, basic, gene 5 [Mus musculus] 30 (30 0 0 0 0) 1.41E+01 61766.29 20911031 protease, serine, 1 [Mus musculus] 74 (74 0 0 0 0) 8.10E+00 26134.54 16716569 keratin complex 1, acidic, gene 16 [Mus musculus] 10 (10 0 0 0 0) 1.26E+01 51606.09 6680604 RAB2, member RAS oncogene family [Mus musculus] 1 (1 0 0 0 0) 7.50E+00 23547.37 10946940 calcium/calmodulin-dependent protein kinase II alpha isoform 2 3 (3 0 0 0 0) 7.50E+00 54114.39 28916677 [Mus musculus] PREDICTED: similar to Ig kappa chain V-I region HK102 1 (1 0 0 0 0) 1.33E+01 13302.18 94378736 precursor [Mus musculus] RAB11B, member RAS oncogene family [Mus musculus] 1 (1 0 0 0 0) 5.00E+00 24489.30 6679583 hypothetical protein LOC52637 [Mus musculus] 1 (1 0 0 0 0) 1.39E+01 12096.88 19527228 synaptosomal-associated protein 25 [Mus musculus] 5 (5 0 0 0 0) 2.14E+01 23314.99 6755588 malate dehydrogenase 1, NAD (soluble) [Mus musculus] 4 (4 0 0 0 0) 1.65E+01 36467.88 31982178 histone 1, H4m [Mus musculus] 12 (12 0 0 0 0) 5.05E+01 11367.26 30089708 plakophilin 1 [Mus musculus] 1 (1 0 0 0 0) 2.10E+00 80895.76 9790161 3-monooxgenase/tryptophan 5-monooxygenase activation protein, 3 (3 0 0 0 0) 1.42E+01 28302.40 31543976 gamma polypeptide [Mus musculus] BM88 antigen [Mus musculus] 1 (1 0 0 0 0) 1.07E+01 14986.83 10946620 cytochrome c-1 [Mus musculus] 1 (1 0 0 0 0) 7.40E+00 35327.41 13385006 histone 3, H2ba [Mus musculus] 1 (1 0 0 0 0) 1.19E+01 13994.10 13386452 1 keratin 17n [Mus musculus] 15 (15 0 0 0 0) 1.33E+01 50176.82 47679095 NADH dehydrogenase (ubiquinone) Fe-S protein 1 [Mus 1 (1 0 0 0 0) 2.20E+00 79748.34 21704020 musculus] neural cell adhesion molecule 1 [Mus musculus] 1 (1 0 0 0 0) 1.50E+00 80295.53 18450276 glial fibrillary acidic protein [Mus musculus] 6 (6 0 0 0 0) 7.70E+00 49899.70 84000448 claudin 11 [Mus musculus] 1 (1 0 0 0 0) 6.80E+00 22114.23 6679186 Tesp4 protein [Mus musculus] 5 (5 0 0 0 0) 1.14E+01 26276.70 51010909 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14) 1 (1 0 0 0 0) 1.30E+01 15282.71 13385492 [Mus musculus] thymus cell antigen 1, theta [Mus musculus] 2 (2 0 0 0 0) 1.60E+01 18079.82 6678347 keratin complex 2, basic, gene 39 [Mus musculus] 11 (11 0 0 0 0) 8.00E+00 61358.33 51092293 keratin complex 2, basic, gene 17 [Mus musculus] 22 (22 0 0 0 0) 1.12E+01 70976.52 46275808 PREDICTED: similar to hemoglobin, beta adult major chain [Mus 4 (4 0 0 0 0) 6.84E+01 3981.69 94381090 musculus] hypothetical protein LOC66152 [Mus musculus] 1 (1 0 0 0 0) 2.66E+01 7445.47 37574048 keratin complex 2, basic, gene 4 [Mus musculus] 8 (8 0 0 0 0) 4.80E+00 56444.18 6678645 ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 (1 0 0 0 0) 5.10E+00 29367.42 13385168 1 [Mus musculus] keratin complex 1, acidic, gene 15 [Mus musculus] 16 (16 0 0 0 0) 1.02E+01 49159.20 6680602 keratin complex 2, basic, gene 10 [Mus musculus] 2 (2 0 0 0 0) 6.60E+00 53251.10 74315985 keratin complex 2, basic, gene 6a [Mus musculus] 8 (8 0 0 0 0) 5.80E+00 59334.75 54607171 PREDICTED: similar to Hemoglobin epsilon-Y2 subunit 2 (2 0 0 0 0) 6.80E+00 16136.49 94381431 (Hemoglobin epsilon-Y2 chain) (Epsilon-Y2-globin) isoform 3 [Mus musculus] clathrin, heavy polypeptide (Hc) [Mus musculus] 4 (4 0 0 0 0) 3.10E+00 191554.60 51491845 vimentin [Mus musculus] 5 (5 0 0 0 0) 1.44E+01 53687.30 31982755 syntaxin 1B2 [Mus musculus] 1 (1 0 0 0 0) 4.90E+00 33244.50 13259378 Na+/K+ -ATPase beta 1 subunit [Mus musculus] 1 (1 0 0 0 0) 4.30E+00 35194.30 6753138 junction plakoglobin [Mus musculus] 8 (8 0 0 0 0) 1.25E+01 81800.32 28395018 PREDICTED: similar to keratin Kb40 [Mus musculus] 3 (3 0 0 0 0) 3.10E+00 44423.74 94411100 glycoprotein m6b [Mus musculus] 1 (1 0 0 0 0) 4.80E+00 29499.13 12963495 keratin complex 2, basic, gene 6g [Mus musculus] 2 (2 0 0 0 0) 4.60E+00 57382.18 9910294 ubiquinol cytochrome c reductase core protein 2 [Mus musculus] 8 (8 0 0 0 0) 1.79E+01 48234.55 22267442 olfactory receptor 507 [Mus musculus] 1 (1 0 0 0 0) 7.60E+00 34823.80 22129355 apolipoprotein E [Mus musculus] 2 (2 0 0 0 0) 8.00E+00 35852.30 6753102 myelin basic protein isoform 1 [Mus musculus] 1 (1 0 0 0 0) 0.00E+00 21502.05 69885032 citrate synthase [Mus musculus] 1 (1 0 0 0 0) 3.40E+00 51736.39 13385942 P lysozyme structural [Mus musculus] 3 (3 0 0 0 0) 8.10E+00 16794.13 7305247 PREDICTED: similar to ADP/ATP translocase 2 (Adenine 2 (2 0 0 0 0) 7.40E+00 32876.02 63475897 nucleotide translocator 2) (ANT 2) (ADP,ATP carrier protein 2) (Solute carrier family 25 member 5) [Mus musculus] ubiquinol-cytochrome c reductase binding protein [Mus musculus] 1 (1 0 0 0 0) 9.00E+00 13561.39 13385726 PREDICTED: similar to Annexin A2 (Annexin II) (Lipocortin II) 4 (4 0 0 0 0) 1.29E+01 32598.86 63594732 (Calpactin I heavy chain) (Chromobindin-8) (p36) (Protein I) (Placental anticoagulant protein IV) (PAP-IV) [Mus musculus] PREDICTED: similar to nonspecific cytotoxic cell receptor protein 1 (1 0 0 0 0) 3.80E+00 33027.25 82904314 1 [Mus musculus] PREDICTED: similar to type I hair keratin KA28 [Mus musculus] 5 (5 0 0 0 0) 8.90E+00 49457.46 82936608 synaptophysin [Mus musculus] 1 (1 0 0 0 0) 4.20E+00 33353.48 6678195 synaptogyrin 1 isoform 1a [Mus musculus] 1 (1 0 0 0 0) 5.10E+00 25652.55 46877048 PREDICTED: similar to desmoplakin isoform I isoform 3 [Mus 5 (5 0 0 0 0) 2.00E+00 329414.10 94394910 musculus] guanine nucleotide binding protein, alpha o [Mus musculus] 2 (2 0 0 0 0) 4.20E+00 40084.31 6754012 voltage-dependent anion channel 1 [Mus musculus] 3 (3 0 0 0 0) 9.20E+00 30755.25 6755963 2 glycoprotein m6a [Mus musculus] 3 (3 0 0 0 0) 1.29E+01 31149.29 23957686 cytochrome c oxidase subunit IV isoform 1 [Mus musculus] 2 (2 0 0 0 0) 1.42E+01 19530.35 6753498 keratin 13 [Mus musculus] 1 (1 0 0 0 0) 2.10E+00 47753.80 6754480 cytochrome c oxidase subunit II [Mus musculus] 1 (1 0 0 0 0) 8.80E+00 25976.27 34538601 tubulin, beta, 2 [Mus musculus] 3 (3 0 0 0 0) 3.40E+00 49830.70 22165384 ubiquinol-cytochrome c reductase core protein 1 [Mus musculus] 2 (2 0 0 0 0) 4.60E+00 52851.48 46593021 ATP synthase, H+ transporting, mitochondrial F0 complex, 1 (1 0 0 0 0) 1.30E+01 18749.32 21313679 subunit d [Mus musculus] vacuolar H+ ATPase E1 [Mus musculus] 1 (1 0 0 0 0) 6.20E+00 26157.24 45504359 ATP synthase, H+ transporting, mitochondrial F1F0 complex, 2 (2 0 0 0 0) 2.11E+01 8235.54 83715998 subunit e [Mus musculus] keratin complex 2, basic, gene 35 [Mus musculus] 8 (8 0 0 0 0) 6.00E+00 56749.93 47523977 PREDICTED: similar to H3 histone, family 3B [Mus musculus] 3 (3 0 0 0 0) 1.91E+01 15323.85 94396414 keratin complex 1, acidic, gene 1 [Mus musculus] 3 (3 0 0 0 0) 7.90E+00 47112.19 6754484 glutathione S-transferase, mu 1 [Mus musculus] 1 (1 0 0 0 0) 5.50E+00 25969.83 6754084 NADH dehydrogenase (ubiquinone)