CKB, CPTAC-476 - 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.
Protein Sequence hover to view complete sequence
non-CPTAC-3977: View additional DLFDPIIEER data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MPFSNSHNAL | KLRFPAEDEF | PDLSAHNNHM | AKVLTPELYA | ELRAKSTPSG |
| 60 | 70 | 80 | 90 | 100 |
| FTLDDVIQTG | VDNPGHPYIM | TVGCVAGDEE | SYEVFKDLFD | PIIEDRHGGY |
| 110 | 120 | 130 | 140 | 150 |
| KPSDEHKTDL | NPDNLQGGDD | LDPNYVLSSR | VRTGRSIRGF | CLPPHCSRGE |
| 160 | 170 | 180 | 190 | 200 |
| RRAIEKLAVE | ALSSLDGDLA | GRYYALKSMT | EAEQQQLIDD | HFLFDKPVSP |
| 210 | 220 | 230 | 240 | 250 |
| LLLASGMARD | WPDARGIWHN | DNKTFLVWVN | EEDHLRVISM | QKGGNMKEVF |
| 260 | 270 | 280 | 290 | 300 |
| TRFCTGLTQI | ETLFKSKDYE | FMWNPHLGYI | LTCPSNLGTG | LRAGVHIKLP |
| 310 | 320 | 330 | 340 | 350 |
| NLGKHEKFSE | VLKRLRLQKR | GTGGVDTAAV | GGVFDVSNAD | RLGFSEVELV |
| 360 | 370 | 380 | 381 | |
| QMVVDGVKLL | IEMEQRLEQG | QAIDDLMPAQ | K |
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-477 Collapse assay details
Data source: Panorama
Official Gene Symbol
CKB
Peptide Sequence
LAVEALSSLDGDLAGR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
157
Peptide End
172
CPTAC ID
CPTAC-477
Peptide Molecular Mass
1,585.8312
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim
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 Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. 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
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 |
| y11 (1+) | 11.9 | 10.2 | 11.1 | 18.1 | 14.9 | 22.7 | 21.7 | 18.1 | 25.3 | 25 | 15 | 15 |
| y10 (1+) | 10.5 | 7.1 | 7.2 | 19.2 | 15.5 | 22.7 | 21.9 | 17 | 23.8 | 25 | 15 | 15 |
| y9 (1+) | 10.7 | 8.9 | 11 | 20.9 | 14.2 | 19.7 | 23.5 | 16.8 | 22.6 | 25 | 15 | 15 |
| sum | 10.2 | 6.9 | 7.9 | 19.2 | 14.6 | 21.3 | 21.7 | 16.1 | 22.7 | 25 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-476 Collapse assay details
Data source: Panorama
Official Gene Symbol
CKB
Peptide Sequence
VLTPELYAELR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
33
Peptide End
43
CPTAC ID
CPTAC-476
Peptide Molecular Mass
1,302.7184
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim
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 Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. 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
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 |
| y9 (1+) | 6.4 | 10.6 | 10.2 | 9.9 | 11.8 | 11.7 | 11.8 | 15.9 | 15.5 | 15 | 25 | 15 |
| y8 (1+) | 9.5 | 8.4 | 6.2 | 12 | 10.6 | 9.1 | 15.3 | 13.5 | 11 | 15 | 25 | 15 |
| y6 (1+) | 15.6 | 11.1 | 14.5 | 16.9 | 12.3 | 15.1 | 23 | 16.6 | 20.9 | 15 | 25 | 15 |
| sum | 6.4 | 8.7 | 8.1 | 10.5 | 10.4 | 9.4 | 12.3 | 13.6 | 12.4 | 15 | 25 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-3977 Collapse assay details
Data source: Panorama
Official Gene Symbol
Ckb
Peptide Sequence
DLFDPIIEER
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
87
Peptide End
96
CPTAC ID
non-CPTAC-3977
Peptide Molecular Mass
1,245.6241
Species
Mus musculus (Mouse)
Assay Type
Direct MRM
Matrix
Plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Agilent 6490/6495 QQQ
Internal Standard
synthetic peptide
Peptide Standard Purity
>80%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/min
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 |
| y6 (1+) | 3.1 | 1.8 | 0.9 | 6.9 | 4.3 | 3 | 7.6 | 4.7 | 3.1 | 15 | 15 | 15 |
| y8 (2+) | 6.2 | 1.8 | 1.9 | 10.7 | 3.7 | 3.3 | 12.4 | 4.1 | 3.8 | 15 | 15 | 15 |
| y6 (2+) | 5.8 | 1.9 | 1.8 | 8.6 | 5.3 | 3.4 | 10.4 | 5.6 | 3.8 | 15 | 15 | 15 |
| b2 (1+) | 23.7 | 5.7 | 2.8 | 28.4 | 7.8 | 3.6 | 37 | 9.7 | 4.6 | 15 | 15 | 15 |
| b4 (1+) | 7.9 | 2.2 | 1.3 | 9.5 | 5 | 3.6 | 12.4 | 5.5 | 3.8 | 15 | 15 | 15 |
| sum | 2.3 | 1.1 | 0.6 | 6.7 | 4.2 | 3 | 7.1 | 4.3 | 3.1 | 15 | 15 | 15 |