Show Nav →
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.

PAFAH1B1

Previous Assay Next Assay
Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
PAFAH1B1 LIS1, MDCR, MDS, PAFAHA
Sequence Length (AA) Molecular Weight (Da)
410 46638
Protein Name
Platelet-activating factor acetylhydrolase IB subunit alpha
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MVLSQRQRDE LNRAIADYLR SNGYEEAYSV FKKEAELDVN EELDKKYAGL
60 70 80 90 100
LEKKWTSVIR LQKKVMELES KLNEAKEEFT SGGPLGQKRD PKEWIPRPPE
110 120 130 140 150
KYALSGHRSP VTRVIFHPVF SVMVSASEDA TIKVWDYETG DFERTLKGHT
160 170 180 190 200
DSVQDISFDH SGKLLASCSA DMTIKLWDFQ GFECIRTMHG HDHNVSSVAI
210 220 230 240 250
MPNGDHIVSA SRDKTIKMWE VQTGYCVKTF TGHREWVRMV RPNQDGTLIA
260 270 280 290 300
SCSNDQTVRV WVVATKECKA ELREHEHVVE CISWAPESSY SSISEATGSE
310 320 330 340 350
TKKSGKPGPF LLSGSRDKTI KMWDVSTGMC LMTLVGHDNW VRGVLFHSGG
360 370 380 390 400
KFILSCADDK TLRVWDYKNK RCMKTLNAHE HFVTSLDFHK TAPYVVTGSV
410
DQTVKVWECR

Data source: UniProt

Protein Map Collapse protein map

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

Uniprot Database Entry PhosphoSitePlus ®

Click a point on a node
to view detailed assay information below
All other points link out to UniProt


Phosphorylation Acetylation Ubiquitylation Other

loading

Loader

Assay Details for CPTAC-104 Collapse assay details

Data source: Panorama

Official Gene Symbol
PAFAH1B1
Peptide Sequence
TAPYVVTGSVDQTVK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
391
Peptide End
405
CPTAC ID
CPTAC-104
Peptide Molecular Mass
1,563.8144
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
y10 (1+) 8.8 7 5 10.2 8.9 8 13.5 11.3 9.4 15 25 15
y9 (1+) 12 5.8 6.5 19.3 7.3 6.7 22.7 9.3 9.3 15 25 15
y8 (1+) 13.4 9.1 6.6 17.1 9.3 7.5 21.7 13 10 15 25 15
sum 5.5 6.1 4.4 9.5 7.4 5.5 11 9.6 7 15 25 15

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

Additional Resources and Comments

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

Assay Details for CPTAC-103 Collapse assay details

Data source: Panorama

Official Gene Symbol
PAFAH1B1
Peptide Sequence
VWDYETGDFER
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
134
Peptide End
144
CPTAC ID
CPTAC-103
Peptide Molecular Mass
1,415.5994
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
y9 (1+) 10.1 8.2 5.4 14.2 8.1 4.7 17.4 11.5 7.2 15 25 15
y8 (1+) 14.5 10.2 13.5 19.5 10.4 12.6 24.3 14.6 18.5 15 25 15
y6 (1+) 9.8 11.3 11.4 16.4 10.2 11.7 19.1 15.2 16.3 15 25 15
sum 7.2 7.7 6.2 12.5 7.8 5.6 14.4 11 8.4 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
y6 (1+) -0.87 -0.93 -1.19 -1.15 -0.74 -2.12 -1.33 -4.23
y9 (1+) -0.91 -1.03 -1.38 -1.19 -0.91 -1.68 -1.38 -3.73
y8 (1+) -0.93 -0.8 -1.12 -0.9 -0.78 -1.51 -1.06 -2.72
sum -0.9 -0.95 -1.26 -1.11 -0.84 -1.73 -1.29 -3.54

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
y9 (1+) 2.9 9.4 9.9 NA 6.1
y8 (1+) 4.8 6.3 3 NA 1.8
y6 (1+) 13 5.8 17.3 NA 3.4
sum 4.4 2.8 9.5 NA 2.6
Fragment ion / Transition all_intra_CV all_inter_CV
y9 (1+) 7.5 6.7
y8 (1+) 4.4 4.8
y6 (1+) 9.1 10
sum 4.4 4.5

Endogenous

Data source: Panorama

view larger image
Fragment ion / Transition intra_CV inter_CV total_CV
y8 (1+) 10 10.1 14.2
y9 (1+) 8.3 8.3 11.7
y6 (1+) 11.5 9.9 15.2
sum 7.7 7.9 11

Additional Resources and Comments

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