PAFAH1B1, CPTAC-103 - CPTAC Assay Portal
- ️ABCC's Scientific Web Programming Group, Frederick National Laboratory for Cancer Research (FNLCR)
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 |
|---|---|
| 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
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
loading
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
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| Average intra-assay CV (within day CV) |
Average inter-assay CV (between day CV) |
Total CV |
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
| 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
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
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| Average intra-assay CV (within day CV) |
Average inter-assay CV (between day CV) |
Total CV |
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
| 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
| 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
| 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 |