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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.

TRIM28

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
TRIM28 KAP1, RNF96, TIF1B
Sequence Length (AA) Molecular Weight (Da)
835 88550
Protein Name
Transcription intermediary factor 1-beta
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MAASAAAASA AAASAASGSP GPGEGSAGGE KRSTAPSAAA SASASAAASS
60 70 80 90 100
PAGGGAEALE LLEHCGVCRE RLRPEREPRL LPCLHSACSA CLGPAAPAAA
110 120 130 140 150
NSSGDGGAAG DGTVVDCPVC KQQCFSKDIV ENYFMRDSGS KAATDAQDAN
160 170 180 190 200
QCCTSCEDNA PATSYCVECS EPLCETCVEA HQRVKYTKDH TVRSTGPAKS
210 220 230 240 250
RDGERTVYCN VHKHEPLVLF CESCDTLTCR DCQLNAHKDH QYQFLEDAVR
260 270 280 290 300
NQRKLLASLV KRLGDKHATL QKSTKEVRSS IRQVSDVQKR VQVDVKMAIL
310 320 330 340 350
QIMKELNKRG RVLVNDAQKV TEGQQERLER QHWTMTKIQK HQEHILRFAS
360 370 380 390 400
WALESDNNTA LLLSKKLIYF QLHRALKMIV DPVEPHGEMK FQWDLNAWTK
410 420 430 440 450
SAEAFGKIVA ERPGTNSTGP APMAPPRAPG PLSKQGSGSS QPMEVQEGYG
460 470 480 490 500
FGSGDDPYSS AEPHVSGVKR SRSGEGEVSG LMRKVPRVSL ERLDLDLTAD
510 520 530 540 550
SQPPVFKVFP GSTTEDYNLI VIERGAAAAA TGQPGTAPAG TPGAPPLAGM
560 570 580 590 600
AIVKEEETEA AIGAPPTATE GPETKPVLMA LAEGPGAEGP RLASPSGSTS
610 620 630 640 650
SGLEVVAPEG TSAPGGGPGT LDDSATICRV CQKPGDLVMC NQCEFCFHLD
660 670 680 690 700
CHLPALQDVP GEEWSCSLCH VLPDLKEEDG SLSLDGADST GVVAKLSPAN
710 720 730 740 750
QRKCERVLLA LFCHEPCRPL HQLATDSTFS LDQPGGTLDL TLIRARLQEK
760 770 780 790 800
LSPPYSSPQE FAQDVGRMFK QFNKLTEDKA DVQSIIGLQR FFETRMNEAF
810 820 830 835
GDTKFSAVLV EPPPMSLPGA GLSSQELSGG PGDGP

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-446 Collapse assay details

Data source: Panorama

Official Gene Symbol
TRIM28
Peptide Sequence
LDLDLTADSQPPVFK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
493
Peptide End
507
CPTAC ID
CPTAC-446
Peptide Molecular Mass
1,657.8563
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
y10 (1+) 8.6 4.9 6.5 12 14.5 19.1 14.8 15.3 20.2 25 15 15
y9 (1+) 10.1 6.4 7.1 20.1 19.6 22.9 22.5 20.6 24 25 15 15
y8 (1+) 12.5 7.2 6.8 22.8 20 21 26 21.3 22.1 25 15 15
sum 6.9 4.8 6.3 13 16.9 20.5 14.7 17.6 21.4 25 15 15

Additional Resources and Comments

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

Assay Details for CPTAC-447 Collapse assay details

Data source: Panorama

Official Gene Symbol
TRIM28
Peptide Sequence
LSPPYSSPQEFAQDVGR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
751
Peptide End
767
CPTAC ID
CPTAC-447
Peptide Molecular Mass
1,876.8955
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
y10 (1+) 10.5 7.7 3.8 16.5 8.7 5.1 19.6 11.6 6.4 15 25 15
y15 (2+) 4.8 5.7 4.2 11.2 6.9 11.8 12.2 8.9 12.5 15 25 15
y14 (2+) 19.9 9.2 6.3 20.2 9.9 9.5 28.4 13.5 11.4 15 25 15
sum 4.8 5.7 4 10.1 7 10.9 11.2 9 11.6 15 25 15

Additional Resources and Comments

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