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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.

PDCD6IP

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
PDCD6IP AIP1, ALIX, KIAA1375
Sequence Length (AA) Molecular Weight (Da)
868 96023
Protein Name
Programmed cell death 6-interacting protein
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MATFISVQLK KTSEVDLAKP LVKFIQQTYP SGGEEQAQYC RAAEELSKLR
60 70 80 90 100
RAAVGRPLDK HEGALETLLR YYDQICSIEP KFPFSENQIC LTFTWKDAFD
110 120 130 140 150
KGSLFGGSVK LALASLGYEK SCVLFNCAAL ASQIAAEQNL DNDEGLKIAA
160 170 180 190 200
KHYQFASGAF LHIKETVLSA LSREPTVDIS PDTVGTLSLI MLAQAQEVFF
210 220 230 240 250
LKATRDKMKD AIIAKLANQA ADYFGDAFKQ CQYKDTLPKE VFPVLAAKHC
260 270 280 290 300
IMQANAEYHQ SILAKQQKKF GEEIARLQHA AELIKTVASR YDEYVNVKDF
310 320 330 340 350
SDKINRALAA AKKDNDFIYH DRVPDLKDLD PIGKATLVKS TPVNVPISQK
360 370 380 390 400
FTDLFEKMVP VSVQQSLAAY NQRKADLVNR SIAQMREATT LANGVLASLN
410 420 430 440 450
LPAAIEDVSG DTVPQSILTK SRSVIEQGGI QTVDQLIKEL PELLQRNREI
460 470 480 490 500
LDESLRLLDE EEATDNDLRA KFKERWQRTP SNELYKPLRA EGTNFRTVLD
510 520 530 540 550
KAVQADGQVK ECYQSHRDTI VLLCKPEPEL NAAIPSANPA KTMQGSEVVN
560 570 580 590 600
VLKSLLSNLD EVKKEREGLE NDLKSVNFDM TSKFLTALAQ DGVINEEALS
610 620 630 640 650
VTELDRVYGG LTTKVQESLK KQEGLLKNIQ VSHQEFSKMK QSNNEANLRE
660 670 680 690 700
EVLKNLATAY DNFVELVANL KEGTKFYNEL TEILVRFQNK CSDIVFARKT
710 720 730 740 750
ERDELLKDLQ QSIAREPSAP SIPTPAYQSS PAGGHAPTPP TPAPRTMPPT
760 770 780 790 800
KPQPPARPPP PVLPANRAPS ATAPSPVGAG TAAPAPSQTP GSAPPPQAQG
810 820 830 840 850
PPYPTYPGYP GYCQMPMPMG YNPYAYGQYN MPYPPVYHQS PGQAPYPGPQ
860 868
QPSYPFPQPP QQSYYPQQ

Data source: UniProt

Protein Map Collapse protein map

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

Uniprot Database Entry PhosphoSitePlus ®

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All other points link out to UniProt


Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-420 Collapse assay details

Data source: Panorama

Official Gene Symbol
PDCD6IP
Peptide Sequence
SVIEQGGIQTVDQLIK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
423
Peptide End
438
CPTAC ID
CPTAC-420
Peptide Molecular Mass
1,726.9465
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Broad Institute and FHCRC
Submitting Lab PI
Steve Carr

Publication

View Details (opens in a new window)

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253

Response curves acquired at Broad Institute. Repeatability data acquired at Fred Hutchinson Cancer Research Center.

Response curves acquired at Broad Institute. Repeatability data acquired at Fred Hutchinson Cancer Research Center.

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 nL / min

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

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Repeatability

Data source: Panorama

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  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y11 (1+) 6.5 4.9 4 18.8 6.3 3.8 19.9 8 5.5 25 15 15
y10 (1+) 11.6 8.2 8.9 20.9 8.8 10.5 23.9 12 13.8 25 15 15
y8 (1+) 9.8 5.7 8.1 20.5 8.9 6.4 22.7 10.6 10.3 25 15 15
sum 4.8 4.5 4.4 18.5 6.6 3.7 19.1 8 5.7 25 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments

Assay Details for CPTAC-419 Collapse assay details

Data source: Panorama

Official Gene Symbol
PDCD6IP
Peptide Modified Sequence
YYDQIC[+57.0]SIEPK
Modification Type
Carbamidomethyl Cysteine
Protein - Site of Modification
76
Peptide - Site of Modification
6
Peptide Start
71
Peptide End
81
CPTAC ID
CPTAC-419
Peptide Molecular Mass
1,414.6439
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Broad Institute and FHCRC
Submitting Lab PI
Steve Carr

Publication

View Details (opens in a new window)

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253

Response curves acquired at Broad Institute. Repeatability data acquired at Fred Hutchinson Cancer Research Center.

Response curves acquired at Broad Institute. Repeatability data acquired at Fred Hutchinson Cancer Research Center.

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 nL / min

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

view larger image
view larger image
view larger image

Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y9 (1+) 40.5 6.9 16.2 62 9.8 22.3 74.1 12 27.6 15 25 15
y7 (1+) 34.2 9.8 14.8 47.7 12.6 16.8 58.7 16 22.4 15 25 15
y6 (1+) 40.5 6.2 16 60.2 10.7 29.5 72.6 12.4 33.6 15 25 15
sum 38.3 6.2 14.9 56.8 10.1 21.5 68.5 11.9 26.2 15 25 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments