Table 1. List of proteins identified (in at least two out of three nano-LC MALDI-TOF/TOF-MS analyses and at least one peptide sequenced) in one type of BCECs and not in the other.
| Protein Name | Swiss-Prot Accesion | Gene Name | Accession Number | Molecular Weight (Da) | Isoelectric Point | Identification Scorea | Sequence Coverage (%) | Number of fragmented peptides | Number of fraction | Identified only inb |
| Abhydrolase domain-containing protein 14B | ABHEB_BOVIN | ABHD14B | A7YY28 | 22 441 | 6,05 | 43,9 | 13 | 2 | 2 | Re-ind. BBB |
| ADP-ribosylation factor 4 | ARF4_BOVIN | ARF4 | Q3SZF2 | 20 515 | 5,91 | 159,7 | 20,11 | 2 | 2 | Re-ind. BBB |
| EH domain-containing protein 1 | EHD1_BOVIN | EHD1 | Q5E9R3 | 60 644 | 6,4 | 75,7 | 4,66 | 2 | 2 | Re-ind. BBB |
| Dolichyl-diphosphooligosaccharide–protein glycosyltransferase 48 kDa subunit | OST48_BOVIN | DDOST | A6QPY0 | 48 761 | 5,52 | 40,7 | 3,41 | 1 | 2 | Re-ind. BBB |
| Alkaline phosphatase, tissue-nonspecific isozyme | PPBT_BOVIN | ALPL | P09487 | 57 156 | 6,28 | 42,5 | 6,1 | 2 | 2 | Re-ind. BBB |
| SUMO-activating enzyme subunit 1 | SAE1_BOVIN | SAE1 | A2VE14 | 38 281 | 5,15 | 84,3 | 2,77 | 1 | 2 | Re-ind. BBB |
| Splicing factor, arginine/serine-rich 9 | SFRS9_RAT | SFRS9 | Q5PPI1 | 25 482 | 8,67 | 33,5 | 5,42 | 1 | 2 | Re-ind. BBB |
| Structural maintenance of chromosomes flexible hinge domain-containing protein 1 | SMHD1_MOUSE | SMCHD1 | Q6P5D8 | 225 506 | 6,87 | 41,2 | 2,7 | 2 | 2 | Re-ind. BBB |
| Thioredoxin-related transmembrane protein 2 | TMX2_BOVIN | TMX2 | Q2TBU2 | 34 007 | 8,89 | 89,4 | 5 | 1 | 2 | Re-ind. BBB |
| Tropomyosin alpha-1 chain | TPM1_BOVIN | TPM1 | Q5KR49 | 32 675 | 4,69 | 48,1 | 2,77 | 1 | 3 | Re-ind. BBB |
| Xanthine dehydrogenase/oxidase | XDH_BOVIN | XDH | P80457 | 146 696 | 7,97 | 116,5 | 3,23 | 3 | 3 | Re-ind. BBB |
| 26S protease regulatory subunit 6A | PRS6A_RAT | Psmc3 | Q63569 | 49 129 | 5,13 | 45,1 | 3,64 | 1 | 2 | Lim. BBB |
| Class I histocompatibility antigen, GOGO-A0101 alpha chain | 1A01_GORGO | P30375 | 40 804 | 5,91 | 191,1 | 6,57 | 2 | 2 | Lim. BBB | |
| Abhydrolase domain-containing protein 11 | ABHDB_BOVIN | ABHD11 | Q3SZ73 | 33 527 | 9,55 | 46,7 | 6 | 1 | 3 | Lim. BBB |
| Serum albumin | ALBU_BOVIN | ALB | P02769 | 69 248 | 5,82 | 105,9 | 5,1 | 2 | 3 | Lim. BBB |
| Beta-2-microglobulin | B2MG_BOVIN | B2M | P01888 | 13 668 | 7,79 | 114,8 | 21,18 | 2 | 3 | Lim. BBB |
| Carbohydrate sulfotransferase 7 | CHST7_RAT | Chst7 | Q6XQG8 | 55 057 | 9,9 | 33,4 | 2,47 | 1 | 2 | Lim. BBB |
| Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | COX41_BOVIN | COX4I1 | P00423 | 19 559 | 9,32 | 32,5 | 7,1 | 1 | 2 | Lim. BBB |
| Copine-6 | CPNE6_BOVIN | CPNE6 | O95741 | 61 952 | 5,32 | 53,9 | 5,38 | 2 | 2 | Lim. BBB |
| COP9 signalosome complex subunit 8 | CSN8_RAT | Cops8 | Q6P4Z9 | 23 221 | 5,09 | 52,1 | 17,22 | 2 | 2 | Lim. BBB |
| Drebrin | DREB_RAT | DBN1 | Q07266 | 77 424 | 4,46 | 66 | 6 | 2 | 3 | Lim. BBB |
| Clathrin interactor 1 | EPN4_BOVIN | CLINT1 | A7Z035 | 70 477 | 6,15 | 49,1 | 1 | 1 | 3 | Lim. BBB |
| Serine hydroxymethyltransferase, mitochondrial | GLYM_BOVIN | SHMT2 | Q3SZ20 | 55 570 | 7,62 | 73 | 7,53 | 2 | 2 | Lim. BBB |
| Heterogeneous nuclear ribonucleoprotein R | HNRPR_HUMAN | HNRNPR | O43390 | 70 899 | 8,23 | 49,1 | 3,47 | 2 | 5 | Lim. BBB |
| Isocitrate dehydrogenase [NADP], mitochondrial | IDHP_BOVIN | IDH2 | Q04467 | 50 707 | 8,88 | 51,6 | 4,86 | 2 | 3 | Lim. BBB |
| Protein KIAA0284 | K0284_MOUSE | Kiaa0284 | Q80U49 | 170 718 | 6,42 | 34,8 | 2,7 | 2 | 2 | Lim. BBB |
| UMP-CMP kinase | KCY_BOVIN | CMPK1 | Q2KIW9 | 22 265 | 5,66 | 55,5 | 6,12 | 1 | 2 | Lim. BBB |
| U6 snRNA-associated Sm-like protein LSm7 | LSM7_HUMAN | LSM7 | Q9UK45 | 11 595 | 5,1 | 72,9 | 24,27 | 2 | 2 | Lim. BBB |
| Microtubule-associated protein 4 | MAP4_BOVIN | MAP4 | P36225 | 111 846 | 4,85 | 73,7 | 2,14 | 1 | 2 | Lim. BBB |
| Malignant fibrous histiocytoma-amplified sequence 1 | MFHA1_HUMAN | MFHAS1 | Q9Y4C4 | 116 838 | 8,02 | 40,8 | 2,7 | 2 | 2 | Lim. BBB |
| Myoferlin | MYOF_HUMAN | MYOF | Q9NZM1 | 233 177 | 5,83 | 95,3 | 0,92 | 1 | 2 | Lim. BBB |
| NHL repeat-containing protein 3 | NHLC3_MOUSE | NHLRC3 | Q8CCH2 | 38 171 | 5,81 | 47,8 | 3 | 1 | 2 | Lim. BBB |
| Protein NipSnap homolog 2 | NIPS2_HUMAN | GBAS | O75323 | 33 721 | 9,42 | 53,9 | 6 | 1 | 2 | Lim. BBB |
| Prolyl 4-hydroxylase subunit alpha-2 | P4HA2_MOUSE | P4HA2 | Q60716 | 60 964 | 5,55 | 175,8 | 13,96 | 5 | 8 | Lim. BBB |
| Delta-1-pyrroline-5-carboxylate synthetase | P5CS_HUMAN | ALDH18A1 | P54886 | 87 248 | 6,66 | 47,2 | 1,5 | 1 | 3 | Lim. BBB |
| Lysophosphatidylcholine acyltransferase 2-B | PCATB_RAT | Aytl1b | Q4V8A1 | 58 526 | 8,71 | 45,2 | 3 | 2 | 2 | Lim. BBB |
| Protein disulfide-isomerase A4 | PDIA4_BOVIN | PDIA4 | Q29RV1 | 72 481 | 4,99 | 50 | 2,79 | 1 | 3 | Lim. BBB |
| PDZ and LIM domain protein 5 | PDLI5_RAT | PDLIM5 | Q62920 | 63 161 | 8,73 | 48,9 | 1,86 | 1 | 3 | Lim. BBB |
| Ribose-phosphate pyrophosphokinase 1 | PRPS1_BOVIN | PRPS2 | Q2HJ58 | 34 812 | 6,51 | 91,5 | 2,7 | 1 | 2 | Lim. BBB |
| 26S protease regulatory subunit S10B | PRS10_BOVIN | PSMC6 | Q2KIW6 | 44 046 | 6,74 | 42 | 5,4 | 2 | 2 | Lim. BBB |
| Ras-related protein Rab-2A | RAB2A_RAT | RAB2A | P05712 | 23 521 | 6,08 | 31,2 | 6,13 | 1 | 2 | Lim. BBB |
| RNA-binding protein Raly | RALY_MOUSE | RALY | Q64012 | 33 138 | 8,94 | 39,8 | 3,52 | 1 | 2 | Lim. BBB |
| 40S ribosomal protein S14 | RS14_RAT | Rps14 | P13471 | 16 249 | 10,07 | 96,2 | 14 | 1 | 2 | Lim. BBB |
| Splicing factor 1 | SF01_HUMAN | SF1 | Q15637 | 68 286 | 9,07 | 67,4 | 5,55 | 1 | 2 | Lim. BBB |
| Sideroflexin-3 | SFXN3_BOVIN | SFXN3 | A6QP55 | 35 685 | 9,66 | 81,2 | 9 | 2 | 3 | Lim. BBB |
| Small nuclear ribonucleoprotein Sm D2 | SMD2_BOVIN | SNRPD2 | Q3SZF8 | 13 518 | 9,92 | 78,8 | 16,1 | 1 | 2 | Lim. BBB |
| Threonyl-tRNA synthetase, cytoplasmic | SYTC_BOVIN | TARS | Q3ZBV8 | 83 439 | 6,34 | 62,7 | 2,9 | 2 | 2 | Lim. BBB |
| Transforming growth factor-beta receptor-associated protein 1 | TGFA1_BOVIN | TGFBRAP1 | Q8WUH2 | 97 096 | 6,1 | 36 | 2,7 | 2 | 2 | Lim. BBB |
| Tax1-binding protein 3 | TX1B3_MOUSE | TAX1BP3 | Q9DBG9 | 13 714 | 8,04 | 104,5 | 14,51 | 1 | 2 | Lim. BBB |
| Vigilin | VIGLN_RAT | HDLBP | Q9Z1A6 | 141 496 | 6,51 | 49,7 | 1,65 | 1 | 3 | Lim. BBB |
a
Identification score: the relevance of protein identities was judged according to the probability-based molecular weight search score [33] (calculated with p<0.05)). The significance threshold of ions scores corresponds to the value of 31.
b
Protein identified in brain capillary endothelial cells displaying limited BBB (Lim. BBB) or re-induced BBB (Re-ind. BBB) functions.