PCDH1, CPTAC-1310 - CPTAC Assay Portal (original) (raw)
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We would like to acknowledge the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) Assay Portal (assays.cancer.gov) for developing assays and establishing criteria for the assays described in this publication.
PCDH1
Protein Sequence hover to view complete sequence
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MDSGAGGRRC | PEAALLILGP | PRMEHLRHSP | GPGGQRLLLP | SMLLALLLLL |
| 60 | 70 | 80 | 90 | 100 |
| APSPGHATRV | VYKVPEEQPP | NTLIGSLAAD | YGFPDVGHLY | KLEVGAPYLR |
| 110 | 120 | 130 | 140 | 150 |
| VDGKTGDIFT | TETSIDREGL | RECQNQLPGD | PCILEFEVSI | TDLVQNGSPR |
| 160 | 170 | 180 | 190 | 200 |
| LLEGQIEVQD | INDNTPNFAS | PVITLAIPEN | TNIGSLFPIP | LASDRDAGPN |
| 210 | 220 | 230 | 240 | 250 |
| GVASYELQAG | PEAQELFGLQ | VAEDQEEKQP | QLIVMGNLDR | ERWDSYDLTI |
| 260 | 270 | 280 | 290 | 300 |
| KVQDGGSPPR | ASSALLRVTV | LDTNDNAPKF | ERPSYEAELS | ENSPIGHSVI |
| 310 | 320 | 330 | 340 | 350 |
| QVKANDSDQG | ANAEIEYTFH | QAPEVVRRLL | RLDRNTGLIT | VQGPVDREDL |
| 360 | 370 | 380 | 390 | 400 |
| STLRFSVLAK | DRGTNPKSAR | AQVVVTVKDM | NDNAPTIEIR | GIGLVTHQDG |
| 410 | 420 | 430 | 440 | 450 |
| MANISEDVAE | ETAVALVQVS | DRDEGENAAV | TCVVAGDVPF | QLRQASETGS |
| 460 | 470 | 480 | 490 | 500 |
| DSKKKYFLQT | TTPLDYEKVK | DYTIEIVAVD | SGNPPLSSTN | SLKVQVVDVN |
| 510 | 520 | 530 | 540 | 550 |
| DNAPVFTQSV | TEVAFPENNK | PGEVIAEITA | SDADSGSNAE | LVYSLEPEPA |
| 560 | 570 | 580 | 590 | 600 |
| AKGLFTISPE | TGEIQVKTSL | DREQRESYEL | KVVAADRGSP | SLQGTATVLV |
| 610 | 620 | 630 | 640 | 650 |
| NVLDCNDNDP | KFMLSGYNFS | VMENMPALSP | VGMVTVIDGD | KGENAQVQLS |
| 660 | 670 | 680 | 690 | 700 |
| VEQDNGDFVI | QNGTGTILSS | LSFDREQQST | YTFQLKAVDG | GVPPRSAYVG |
| 710 | 720 | 730 | 740 | 750 |
| VTINVLDEND | NAPYITAPSN | TSHKLLTPQT | RLGETVSQVA | AEDFDSGVNA |
| 760 | 770 | 780 | 790 | 800 |
| ELIYSIAGGN | PYGLFQIGSH | SGAITLEKEI | ERRHHGLHRL | VVKVSDRGKP |
| 810 | 820 | 830 | 840 | 850 |
| PRYGTALVHL | YVNETLANRT | LLETLLGHSL | DTPLDIDIAG | DPEYERSKQR |
| 860 | 870 | 880 | 890 | 900 |
| GNILFGVVAG | VVAVALLIAL | AVLVRYCRQR | EAKSGYQAGK | KETKDLYAPK |
| 910 | 920 | 930 | 940 | 950 |
| PSGKASKGNK | SKGKKSKSPK | PVKPVEDEDE | AGLQKSLKFN | LMSDAPGDSP |
| 960 | 970 | 980 | 990 | 1000 |
| RIHLPLNYPP | GSPDLGRHYR | SNSPLPSIQL | QPQSPSASKK | HQVVQDLPPA |
| 1010 | 1020 | 1030 | 1040 | 1050 |
| NTFVGTGDTT | STGSEQYSDY | SYRTNPPKYP | SKQVGQPFQL | STPQPLPHPY |
| 1060 | ||||
| HGAIWTEVWE |
Data source: UniProt
Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs
Uniprot Database Entry PhosphoSitePlus ®
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Phosphorylation Acetylation Ubiquitylation Other
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Assay Details for CPTAC-1310 Collapse assay details
Data source: Panorama
Official Gene Symbol
PCDH1
Peptide Modified Sequence
AN[+1.0]DSDQGANAEIEYTFHQAPEVVR
Modification Type
Deamidated (N)
Protein - Site of Modification
305
Peptide - Site of Modification
2
Peptide Start
304
Peptide End
327
CPTAC ID
CPTAC-1310
Peptide Molecular Mass
2,661.1943
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Human ovarian tumor tissue digest
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
TSQ Vantage
Internal Standard
Stable isotope-labeled peptides
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Accela 1250 Quaternary Low Pump
Column Packing
C18, 3 µm, 300 Å
Column Dimensions
1.0 mm I.D. x 15 cm
Flow Rate
50 µL/min
Assay Multiplexing Expand assay panel
Johns Hopkins University-D
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV
| n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 18.7 | 7 | 11 | 21 | 7 | 11.3 | 28.1 | 9.9 | 15.8 | 15 | 15 | 15 |
| y8 (1+) | 17.6 | 9.5 | 12.5 | 20.1 | 9.7 | 10.9 | 26.7 | 13.6 | 16.6 | 15 | 15 | 15 |
| y7 (1+) | 13.3 | 9.1 | 7.5 | 12.4 | 8 | 6.9 | 18.2 | 12.1 | 10.2 | 15 | 15 | 15 |
| sum | 9.9 | 4.4 | 6 | 11.3 | 4.7 | 6 | 15 | 6.4 | 8.5 | 15 | 15 | 15 |