PCDH1, CPTAC-1310 - CPTAC Assay Portal | Office of Cancer Clinical Proteomics Research

Please include the following statement when referencing the CPTAC Assay Portal

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.

Overview Data source: UniProt

Official Gene Symbol	Other Aliases
PCDH1	N/A

Sequence Length (AA)	Molecular Weight (Da)
1060	114743

Protein Name
Protocadherin-1

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

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

Protein Map Collapse protein map

Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Uniprot Database Entry PhosphoSitePlus ®

Click a point on a node

to view detailed assay information below

All other points link out to UniProt

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

CPTAC-1297: SUN1. TLSPTGN[+1.0]ISSAPK	CPTAC-1298: COLGALT1. TALWVATDHNM[+16.0]DN[+1.0]TSTVLR	CPTAC-1299: APOB. FN[+1.0]SSYLQGTNQITGR
CPTAC-1300: APOB. FVEGSHN[+1.0]STVSLTTK	CPTAC-1301: QPCT. YFQN[+1.0]YSYGGVIQDDHIPFLR	CPTAC-1302: CA1. EIINVGHSFHVNFEDNDN[+1.0]R
CPTAC-1303: VIM. QDVDN[+1.0]ASLAR	CPTAC-1304: DPP7. N[+1.0]LSASVIAVTIQGGAHHLDLR	CPTAC-1305: SERPING1. M[+16.0]LFVEPILEVSSLPTTN[+1.0]STTNSATK
CPTAC-1306: CEACAM8. LFIPN[+1.0]ITTK	CPTAC-1307: DSG2. ESFLAPSSGVQPTLAM[+16.0]PNIAVGQN[+1.0]VTVTER	CPTAC-1308: M6PR. LKPLFN[+1.0]K
CPTAC-1309: ACP2. FNPN[+1.0]ISWQPIPVHTVPITEDR	CPTAC-1310: PCDH1. AN[+1.0]DSDQGANAEIEYTFHQAPEVVR	CPTAC-1311: ITGB8. NYAIIKPIGFN[+1.0]ETAK
CPTAC-1312: CALCOCO2. SAN[+1.0]STLAQALHWTR	CPTAC-1313: MINPP1. N[+1.0]ATALYHVEAFK	CPTAC-1314: KRT40. TYN[+1.0]ASVLPVR
CPTAC-1315: MMP23B. ALM[+16.0]HLN[+1.0]ATLR	CPTAC-1316: CD6. EGDN[+1.0]ITLK	CPTAC-1317: CD6. N[+1.0]ATVVWM[+16.0]K
CPTAC-1318: CD6. TVNSLN[+1.0]VSAISIPEHDEADEISDENR	CPTAC-1319: IRAK2. TILVDN[+1.0]NTWNNTHISR	CPTAC-1320: AEN. LN[+1.0]STAQK
CPTAC-1321: PLTP. N[+1.0]WSLPNR	CPTAC-1322: OVGP1. FVPIYGN[+1.0]HSSVNSVTPQTSPLSLK	CPTAC-2612: MMP23B. ALM[+16.0]HLN[+1.0]ATLR

Chromatograms

Data source: Panorama

view larger image

Response Curves

Data source: Panorama

view larger image

Retrieving Data

Repeatability

Data source: Panorama

view larger image

	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

PCDH1

Overview Data source: UniProt

Protein Sequence hover to view complete sequence

Protein Map Collapse protein map

Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Assay Details for CPTAC-1310 Collapse assay details

Assay Parameters Collapse assay parameters

Assay Multiplexing Expand assay panel

Chromatograms

Response Curves

Repeatability

Additional Resources and Comments

Comments

Search form

PCDH1

Overview Data source: UniProt

Protein Sequence hover to view complete sequence

Protein Map Collapse protein map

Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Assay Details for CPTAC-1310 Collapse assay details

Assay Parameters Collapse assay parameters

Assay Multiplexing Expand assay panel

Chromatograms

Response Curves

Repeatability

Additional Resources and Comments

Comments