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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.

HSD17B4

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
HSD17B4 EDH17B4, SDR8C1
Sequence Length (AA) Molecular Weight (Da)
736 79686
Protein Name
Peroxisomal multifunctional enzyme type 2
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MGSPLRFDGR VVLVTGAGAG LGRAYALAFA ERGALVVVND LGGDFKGVGK
60 70 80 90 100
GSLAADKVVE EIRRRGGKAV ANYDSVEEGE KVVKTALDAF GRIDVVVNNA
110 120 130 140 150
GILRDRSFAR ISDEDWDIIH RVHLRGSFQV TRAAWEHMKK QKYGRIIMTS
160 170 180 190 200
SASGIYGNFG QANYSAAKLG LLGLANSLAI EGRKSNIHCN TIAPNAGSRM
210 220 230 240 250
TQTVMPEDLV EALKPEYVAP LVLWLCHESC EENGGLFEVG AGWIGKLRWE
260 270 280 290 300
RTLGAIVRQK NHPMTPEAVK ANWKKICDFE NASKPQSIQE STGSIIEVLS
310 320 330 340 350
KIDSEGGVSA NHTSRATSTA TSGFAGAIGQ KLPPFSYAYT ELEAIMYALG
360 370 380 390 400
VGASIKDPKD LKFIYEGSSD FSCLPTFGVI IGQKSMMGGG LAEIPGLSIN
410 420 430 440 450
FAKVLHGEQY LELYKPLPRA GKLKCEAVVA DVLDKGSGVV IIMDVYSYSE
460 470 480 490 500
KELICHNQFS LFLVGSGGFG GKRTSDKVKV AVAIPNRPPD AVLTDTTSLN
510 520 530 540 550
QAALYRLSGD WNPLHIDPNF ASLAGFDKPI LHGLCTFGFS ARRVLQQFAD
560 570 580 590 600
NDVSRFKAIK ARFAKPVYPG QTLQTEMWKE GNRIHFQTKV QETGDIVISN
610 620 630 640 650
AYVDLAPTSG TSAKTPSEGG KLQSTFVFEE IGRRLKDIGP EVVKKVNAVF
660 670 680 690 700
EWHITKGGNI GAKWTIDLKS GSGKVYQGPA KGAADTTIIL SDEDFMEVVL
710 720 730 736
GKLDPQKAFF SGRLKARGNI MLSQKLQMIL KDYAKL

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-390 Collapse assay details

Data source: Panorama

Official Gene Symbol
HSD17B4
Peptide Sequence
ATSTATSGFAGAIGQK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
316
Peptide End
331
CPTAC ID
CPTAC-390
Peptide Molecular Mass
1,466.7365
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+) 8 6.2 6.1 10.5 11.6 7.4 13.2 13.2 9.6 25 15 15
y10 (1+) 8.7 7.1 5 19.4 12.6 14.3 21.3 14.5 15.1 25 15 15
y9 (1+) 5.8 7.1 6.1 9.3 8.3 8.7 11 10.9 10.6 25 15 15
sum 6.6 5.9 3.6 11.7 9.5 7 13.4 11.2 7.9 25 15 15

Additional Resources and Comments

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

Assay Details for CPTAC-389 Collapse assay details

Data source: Panorama

Official Gene Symbol
HSD17B4
Peptide Sequence
GALVVVNDLGGDFK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
33
Peptide End
46
CPTAC ID
CPTAC-389
Peptide Molecular Mass
1,402.7456
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+) 6 6.1 7.9 10.1 19.9 12.4 11.7 20.8 14.7 15 25 15
y9 (1+) 7.2 4.3 5.9 12.2 19.2 10.5 14.2 19.7 12 15 25 15
y8 (1+) 8.3 7.3 7.1 13.1 18.4 11.3 15.5 19.8 13.3 15 25 15
sum 6.3 4.9 5.8 11.3 19.1 10.4 12.9 19.7 11.9 15 25 15

Additional Resources and Comments

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