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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.

Overview Data source: UniProt

Official Gene Symbol Other Aliases
YBX3 CSDA, DBPA
Sequence Length (AA) Molecular Weight (Da)
372 40090
Protein Name
Y-box-binding protein 3
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MSEAGEATTT TTTTLPQAPT EAAAAAPQDP APKSPVGSGA PQAAAPAPAA
60 70 80 90 100
HVAGNPGGDA APAATGTAAA ASLATAAGSE DAEKKVLATK VLGTVKWFNV
110 120 130 140 150
RNGYGFINRN DTKEDVFVHQ TAIKKNNPRK YLRSVGDGET VEFDVVEGEK
160 170 180 190 200
GAEAANVTGP DGVPVEGSRY AADRRRYRRG YYGRRRGPPR NYAGEEEEEG
210 220 230 240 250
SGSSEGFDPP ATDRQFSGAR NQLRRPQYRP QYRQRRFPPY HVGQTFDRRS
260 270 280 290 300
RVLPHPNRIQ AGEIGEMKDG VPEGAQLQGP VHRNPTYRPR YRSRGPPRPR
310 320 330 340 350
PAPAVGEAED KENQQATSGP NQPSVRRGYR RPYNYRRRPR PPNAPSQDGK
360 370 372
EAKAGEAPTE NPAPPTQQSS AE

Data source: UniProt


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

Uniprot Database Entry PhosphoSitePlus ®

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to view detailed assay information below
All other points link out to UniProt



Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-344 Collapse assay details

Data source: Panorama

Official Gene Symbol
YBX3
Peptide Sequence
DGVPEGAQLQGPVHR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
269
Peptide End
283
CPTAC ID
CPTAC-344
Peptide Molecular Mass
1,558.7852
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


Response Curves

Data source: Panorama

Retrieving Data

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Repeatability

Data source: Panorama

  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
y10 (1+) 32.6 7.9 13.2 33.1 15.8 12.1 46.5 17.7 17.9 15 15 15
y8 (1+) 27.4 9.7 11.1 29.5 14.3 16.2 40.3 17.3 19.6 15 15 15
y7 (1+) 23.1 13.8 10.4 25.9 14.1 14.2 34.7 19.7 17.6 15 15 15
sum 15.1 7 6.6 18.6 10.1 8.1 24 12.3 10.4 15 15 15


Additional Resources and Comments


Assay Details for CPTAC-343 Collapse assay details

Data source: Panorama

Official Gene Symbol
YBX3
Peptide Sequence
GAEAANVTGPDGVPVEGSR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
151
Peptide End
169
CPTAC ID
CPTAC-343
Peptide Molecular Mass
1,781.8544
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


Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

  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
y12 (1+) 11.4 6.1 8.4 19.1 12.6 9 22.2 14 12.3 15 25 15
y11 (1+) 12.3 6 4.7 15.3 8.7 8.1 19.6 10.6 9.4 15 25 15
y10 (1+) 17.9 9.6 4.2 19.9 8.8 4.8 26.8 13 6.4 15 25 15
sum 7 4.6 5.1 15 9.1 7 16.6 10.2 8.7 15 25 15


Additional Resources and Comments