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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.

PSMD3

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
PSMD3 N/A
Sequence Length (AA) Molecular Weight (Da)
534 60978
Protein Name
26S proteasome non-ATPase regulatory subunit 3
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MKQEGSARRR GADKAKPPPG GGEQEPPPPP APQDVEMKEE AATGGGSTGE
60 70 80 90 100
ADGKTAAAAA EHSQRELDTV TLEDIKEHVK QLEKAVSGKE PRFVLRALRM
110 120 130 140 150
LPSTSRRLNH YVLYKAVQGF FTSNNATRDF LLPFLEEPMD TEADLQFRPR
160 170 180 190 200
TGKAASTPLL PEVEAYLQLL VVIFMMNSKR YKEAQKISDD LMQKISTQNR
210 220 230 240 250
RALDLVAAKC YYYHARVYEF LDKLDVVRSF LHARLRTATL RHDADGQATL
260 270 280 290 300
LNLLLRNYLH YSLYDQAEKL VSKSVFPEQA NNNEWARYLY YTGRIKAIQL
310 320 330 340 350
EYSEARRTMT NALRKAPQHT AVGFKQTVHK LLIVVELLLG EIPDRLQFRQ
360 370 380 390 400
PSLKRSLMPY FLLTQAVRTG NLAKFNQVLD QFGEKFQADG TYTLIIRLRH
410 420 430 440 450
NVIKTGVRMI SLSYSRISLA DIAQKLQLDS PEDAEFIVAK AIRDGVIEAS
460 470 480 490 500
INHEKGYVQS KEMIDIYSTR EPQLAFHQRI SFCLDIHNMS VKAMRFPPKS
510 520 530 534
YNKDLESAEE RREREQQDLE FAKEMAEDDD DSFP

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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Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-152 Collapse assay details

Data source: Panorama

Official Gene Symbol
PSMD3
Peptide Sequence
HDADGQATLLNLLLR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
242
Peptide End
256
CPTAC ID
CPTAC-152
Peptide Molecular Mass
1,648.8897
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

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

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
y7 (1+) 10 7.1 2.4 18.2 21 6.1 20.8 22.2 6.6 15 25 15
y6 (1+) 4.7 10 3.2 12.4 15.8 6.8 13.3 18.7 7.5 15 25 15
y5 (1+) 11.5 21.5 3.7 18.2 33.3 8.5 21.5 39.6 9.3 15 25 15
sum 6.9 14.1 3 14.2 19.4 7 15.8 24 7.6 15 25 15

Selectivity

Data source: Panorama

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Slope of Curve Fit for cell line
fragment_ion HCC1187 HCC1419 HCC1954 HCC70 MCF12A MDAMB175VII ZR751 ZR7530
y6 (1+) -0.2 -0.15 -0.1 -0.22 -0.15 -0.12 -0.16 -0.11
y5 (1+) -0.16 -0.13 -0.09 -0.22 -0.15 -0.13 -0.16 -0.1
y7 (1+) -0.16 -0.16 -0.13 -0.26 -0.2 -0.12 -0.16 -0.09
sum -0.18 -0.14 -0.1 -0.23 -0.16 -0.13 -0.16 -0.1

Stability

Data source: Panorama

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Fragment ion / Transition control_intra_CV actual_temp_intra_CV frozen_intra_CV FTx1_intra_CV FTx2_intra_CV
y5 (1+) 27.5 21.7 3.3 NA 13.1
y6 (1+) 14.7 19.5 1.2 NA 15.9
y7 (1+) 23.2 17.3 7.1 NA 15
sum 14.9 20.7 0.9 NA 14.6
Fragment ion / Transition all_intra_CV all_inter_CV
y5 (1+) 17.5 20
y6 (1+) 14.2 12.8
y7 (1+) 16 14.6
sum 14.3 15.8

Endogenous

Data source: Panorama

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Fragment ion / Transition intra_CV inter_CV total_CV
y7 (1+) 7.6 26.4 27.5
y5 (1+) 17.5 28.7 33.6
y6 (1+) 9.9 18.9 21.3
sum 12.9 22.4 25.8

Additional Resources and Comments

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

Assay Details for CPTAC-153 Collapse assay details

Data source: Panorama

Official Gene Symbol
PSMD3
Peptide Sequence
LQLDSPEDAEFIVAK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
426
Peptide End
440
CPTAC ID
CPTAC-153
Peptide Molecular Mass
1,673.8512
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

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

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
y11 (1+) 12.2 8.4 7.4 13.4 11.8 11.3 18.1 14.5 13.5 15 25 15
y10 (1+) 9.7 7.3 9.2 17.7 12.2 9.7 20.2 14.2 13.4 15 25 15
y8 (1+) 40.4 24 19.8 45.2 27.5 19.3 60.6 36.5 27.7 15 25 15
sum 9.5 8.1 4.5 14.6 12.7 5.8 17.4 15.1 7.3 15 25 15

Selectivity

Data source: Panorama

view larger image
Slope of Curve Fit for cell line
fragment_ion HCC1187 HCC1419 HCC1954 HCC70 MCF12A MDAMB175VII ZR751 ZR7530
y11 (1+) -0.25 -0.27 -0.09 -0.37 -0.36 -0.26 -0.27 -0.3
y10 (1+) -0.3 -0.33 -0.15 -0.4 -0.25 -0.18 -0.16 -0.19
y8 (1+) -0.17 -0.45 -0.11 -0.4 -0.34 -0.31 -0.2 -0.16
sum -0.27 -0.31 -0.13 -0.4 -0.29 -0.22 -0.2 -0.22

Stability

Data source: Panorama

view larger image
Fragment ion / Transition control_intra_CV actual_temp_intra_CV frozen_intra_CV FTx1_intra_CV FTx2_intra_CV
Fragment ion / Transition all_intra_CV all_inter_CV

Endogenous

Data source: Panorama

view larger image
Fragment ion / Transition intra_CV inter_CV total_CV
y8 (1+) 25.3 33.8 42.2
y10 (1+) 7.5 12.2 14.3
y11 (1+) 8.7 11.2 14.2
sum 8 12.6 14.9

Additional Resources and Comments

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