Table 1.
Confirmed crosslinked peptides.
| # | Protein | UniProt ID | Mass m/z | Elute Time |
Z | Score + Score Diffa |
% Matchb |
Peptidesc |
|---|---|---|---|---|---|---|---|---|
| First Replicate | ||||||||
| 1 | Kinesin-like protein KIF26B | Q2KJY2 | 672.8934 | 22.88 | 4 | 47.4 + 1.9 | 82.7 | AVNKVKDTPGLGK450VK |
| Hemicentin-1 | Q96RW7 | KGVDIE4391ISHR | ||||||
| 2 | Kinesin-like protein KIF26B | Q2KJY2 | 896.8553 | 22.95 | 3 | 34.2 + 2.4 | 76.8 | AVNKVKDTPGLGK450VK |
| Hemicentin-1 | Q96RW7 | KGVDIE4391ISHR | ||||||
| 3 | Dual specificity mitogen-activated protein kinase kinase 7 | O14733 | 774.4123 | 26.84 | 3 | 29.2 + 8.4 | 51.8 | DVK245PSNILLDER |
| Ankyrin repeat domain-containing protein 12 | Q6UB98 | HLAESKE927K | ||||||
| 4 | Supervillin | O95425 | 835.1508 | 24.16 | 3 | 22.9 + 1.7 | 67.7 | VKVRE308K |
| UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyl transferase-like protein 1 | Q67FW5 | KVVAFCDVDENK298IRK | ||||||
| 5 | Transcription factor 20 | Q9UGU0 | 626.6151 | 24.08 | 4 | 56.6 + 9.1 | 84.6 | VKVRHK1754SASNGSK |
| Myosin-4 | Q9Y623 | VKKQLDHE1540K | ||||||
| 6 | Serine/threonine-protein kinase WNK2 | Q9Y3S1 | 831.2604 | 24.25 | 4 | 43.2 + 3.4 | 82.5 | TVGAAQLK2180PTLNQLKQTQK |
| Oxysterol-binding protein-related protein 5 | Q9H0X9 | VTKKE97TLKAQK | ||||||
| 7 | Tubulin polyglutamylase TTLL7 | Q6ZT98 | 673.1405 | 23.27 | 4 | 34.2 + 4.1 | 57.0 | QRKVLDIVK742TSIR |
| Transcription elongation factor A protein-like 2 | Q9H3H9 | KGKSE83MoxQGGSK | ||||||
| 8 | Gem-associated protein 4 | P57678 | 558.1219 | 23.35 | 5 | 54.6 + 1.6 | 67.9 | NK497VLAGILRSWGRK |
| Lysosomal-trafficking regulator | Q99698 | QD199HPKAKLDR | ||||||
| Second Replicate | ||||||||
| 9 | Kinesin-like protein KIF26B | Q2KJY2 | 672.8947 | 24.04 | 4 | 52.6 + 4.4 | 81.1 | AVNKVKDTPGLGK450VK |
| Hemicentin-1 | Q96RW7 | KGVDIE4391ISHR | ||||||
| 10 | Microcephalin | Q8NEM0 | 538.5172 | 24.111 | 5 | 39.1 + 1.9 | 69.0 | GKKPTRTLVMoxTSMPSE658K |
| Junction-mediating and -regulatory protein | Q8N9B5 | KGVKLK936K | ||||||
| 11 | Centromere protein V-like protein 3 | A0A0U1RRI6 | 626.6141 | 24.54 | 4 | 52.5 + 12.5 | 83.1 | VQVGVGSHAAAK67RWLGK |
| Fibroblast growth factor receptor-like 1 | Q8N441 | VKQVE90R | ||||||
| 12 | Elongation factor 2 | P13639 | 704.9792 | 26.01 | 5 | 50.5 + 16.7 | 64.3 | K16ANIRNMSVIAHVDHGK |
| Protein eva-1 homolog A | Q9H8M9 | NVFTSAE116ELERAQR | ||||||
| 13 | Proteasome subunit alpha type-2 | P25787 | 691.3914 | 21.50 | 5 | 54.2 + 24.6 | 65.1 | QK53SILYDERSVHKVEPITK |
| GTPase-activating protein and VPS9 domain-containing protein 1 | Q14C86 | LNADVLKTAE39K | ||||||
| 14 | Transcriptional regulator ATRX | P46100 | 820.4745 | 26.86 | 4 | 44.2 + 4.2 | 65.0 | ENLLGSIK1774EFR |
| Isoleucine-tRNA ligase, cytoplasmic | P41252 | YPLKEIVVIHQD856PEALK | ||||||
| 15 | Prohibitin-2 | Q99623 | 811.0315 | 24.93 | 5 | 36.0 + 8.6 | 46.0 | QK224IVQAEGEAEAAK |
| Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial | Q96HY7 | TLVFCSGKHFYSLVKQRE821SLGAK | ||||||
| 16 | Oxysterol-binding protein-related protein 5 | Q9H0X9 | 831.0162 | 26.55 | 4 | 36.1 + 2.1 | 68.3 | VTKKE97TLKAQK |
| Serine/threonine-protein kinase WNK2 | Q9Y3S1 | TVGAAQLK2180PTLNQLKQTQK | ||||||
| Third Replicate | ||||||||
| 17 | Kinesin-like protein KIF26B | Q2KJY2 | 538.5171 | 100.77 | 5 | 37.7 + 2.8 | 65.4 | AVNKVKDTPGLGK450VK |
| Hemicentin-1 | Q96RW7 | KGVDIE4391ISHR | ||||||
| 18 | Mitochondrial 10-formyltetrahydrofolate dehydrogenase | Q3SY69 | 538.5169 | 29.11 | 5 | 29.0 + 7.4 | 57.2 | VKGKTIK89EVAEAYR |
| Lysine-specific demethylase 5C | P41229 | VALEVE784DGRK | ||||||
| 19 | DnaJ homolog subfamily C member 9 | Q8WXX5 | 538.5166 | 29.63 | 5 | 43.5 + 1.0 | 69.0 | KRRAQEE196AK |
| Mitochondrial 10-formyl tetrahydrofolate dehydrogenase | Q3SY69 | VKGKTIK89EVAEAYR | ||||||
| 20 | Coatomer subunit delta | P48444 | 538.5165 | 100.27 | 5 | 26.5 + 0 | 58.7 | KGVQLQTHPNVDK335K |
| Kelch domain-containing protein 4 | Q8TBB5 | QRVKKDVD260K | ||||||
| 21 | Kinesin-like protein KIF26B | Q2KJY2 | 672.8947 | 31.55 | 4 | 31.7 + 4.1 | 69.3 | AVNKVKDTPGLGK450VK |
| Hemicentin-1 | Q96RW7 | KGVDIE4391ISHR | ||||||
| 22 | Ankyrin −2 | Q01484 | 672.8947 | 100.84 | 4 | 24.3 + 1.6 | 73.1 | GKVRVEK2031EK |
| C─C motif chemokine 17 | Q92583 | VKNAVKYLQSLE92RS | ||||||
| 23 | Putative high mobility group protein B1-like 1 | B2RPK0 | 672.8946 | 29.11 | 4 | 40.0 + 10.2 | 53.3 | KGVVKAE179K |
| Protein Lines homolog 1 | Q8NG48 | ISLVKTEFHAK113EQYR | ||||||
| 24 | Osteocrin | P61366 | 672.8939 | 29.61 | 4 | 48.6 + 10.5 | 77.9 | QRKVVKHPK113R |
| Helicase-like transcription factor | Q14527 | GKLKNVQSE422TKGLR | ||||||
| 25 | Titin | Q8WZ42 | 626.6149 | 29.44 | 4 | 43.1 + 10.8 | 78.6 | VKVQD28977TPGK |
| Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyl transferase-like protein MGAT4D | A6NG13 | VLNRMK71YEITKR | ||||||
| 26 | StAR-related lipid transfer prot 9 | Q9P1P6 | 671.7452 | 25.80 | 3 | 33.5 + 3.0 | 61.8 | RKKVSFQLE773R |
| Collagen alpha-5(VI) chain | A8TX70 | KGVK1667GPR | ||||||
| 27 | Zinc finger protein 292 | O60281 | 896.8561 | 29.75 | 3 | 32.5 + 4.7 | 69.1 | KRKVE2548K |
| Arginase-2, mitochondrial | P78540 | KGVEHGPAAIREAGLMK56R | ||||||
| 28 | WD repeat-containing protein 1 | O75083 | 872.0002 | 28.52 | 4 | 29.9 + 0.2 | 62.8 | VFASLPQVE16RGVSKIIGGDPK |
| DNA repair protein RAD50 | Q92878 | STESELKKK722EK | ||||||
| 29 | Zinc finger protein 728 | P0DKX0 | 928.9985 | 28.54 | 4 | 46.4 + 6.6 | 65.1 | AIHAGEKLYK481CEECGK |
| Uncharacterized protein C9orf43 | Q8TAL5 | MFLSIHRLTLE269RPALR | ||||||
| 30 | Lysine-specific demethylase 7A | Q6ZMT4 | 736.4008 | 33.85 | 5 | 33.6 + 5.4 | 63.5 | FNKHLQPSSTVPE569WRAKDNDLR |
| Inter-alpha-trypsin inhibitor heavy chain H2 | P19823 | VQISVKK810EK | ||||||
| 31 | Complement receptor type 2 | P20023 | 825.7779 | 26.33 | 3 | 28.0 + 4.9 | 51.3 | LIGEKSLLCITK68DK |
| Oxysterol-binding protein-related protein 9 | Q96SU4 | D680IDAATEAK | ||||||
| 32 | 14-3-3 protein theta | P27348 | 758.4285 | 33.48 | 4 | 44.0 + 1.0 | 66.3 | NLLSVAYK49NVVGGRR |
| Interleukin-10 receptor subunit beta | Q08334 | NILQWE41SPAFAK | ||||||
| 33 | 14-3-3 protein theta | P27348 | 916.2504 | 32.67 | 4 | 39.1 + 5.7 | 56.8 | NLLSVAYK49NVVGGRRSAWR |
| Serologically defined colon cancer antigen 8 | Q86SQ7 | QVLQISEE349ANFEK | ||||||
| 34 | von Willebrand factor A domain-containing protein 3B | Q502W6 | 591.5668 | 27.80 | 4 | 27.2 + 9.0 | 50.2 | D794GLSNASSRR |
| Phosphatidylinositol 4-kinase alpha | P42356 | IHNELSPLK432LR | ||||||
| 35 | Coatomer subunit alpha | P53621 | 606.9457 | 33.54 | 5 | 41.3 + 6.1 | 61.1 | VTTVTEIGK1211DVIGLR |
| Teneurin-4 | Q6N022 | NLLSLDFD1844RVTR | ||||||
| 36 | Microfibrillar-associated protein 1 | P55081 | 835.1493 | 29.59 | 3 | 27.6 + 3.4 | 61.6 | VKVK37RYVSGK |
| Serine/threonine-protein kinase SMG1 | Q96Q15 | KVVD1635NASQGEGVR | ||||||
| 37 | 14-3-3 protein zeta/delta | P63104 | 916.0831 | 34.06 | 5 | 61.4 + 5.3 | 80.9 | SVTEQGAELSNEERNLLSVAY |
| Striated muscle preferentially expressed protein kinase | Q15772 | K49NVVGAR RLFQQKAASLDE538R |
||||||
| 38 | Staphylococcal nuclease domain -containing protein 1 | Q7KZF4 | 847.6662 | 36.73 | 5 | 58.8 + 18.8 | 65.7 | QFQK873VITEYLNAQESAK |
| Zinc finger protein 777 | Q9ULD5 | LAVWAAVQAVE196RKLEAQA MoxR | ||||||
| 39 | C-type lectin domain family 4 member M | Q9H2X3 | 537.6976 | 27.08 | 5 | 37.0 + 2.9 | 56.8 | LQEIYQELTE210LK |
| Betaine-homocysteine S-methyltransferase 1 | Q93088 | ELFEKQK402FK | ||||||
| 40 | Teneurin-3 | Q9P273 | 762.4280 | 31.48 | 4 | 50.0 + 2.2 | 74.4 | NLLSVD1778FDRTTKTEK |
| Rho guanine nucleotide exchange factor 26 | Q96DR7 | RALKEVSK615LVR | ||||||
a
Score and score difference values are assigned by Protein Prospector. The higher the value, the better the match to a theoretical peptide. In Table 1, values range from 24.3 to 61.4.
b
% match is the matched intensity of the assigned peaks compared to the observed peaks. Confidence in the assignment is associated with high % matched intensity.
c
Crosslinked residues are suffixed by a subscripted number identifying the crosslinked residue.