FEN1, CPTAC-700 - CPTAC Assay Portal (original) (raw)
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.
Protein Sequence hover to view complete sequence
CPTAC-1411: View additional LIADVAPSAIR data
CPTAC-1409: View additional SIEEIVR data
CPTAC-700: View additional SIEEIVR data
CPTAC-3230: View additional SIEEIVR data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MGIQGLAKLI | ADVAPSAIRE | NDIKSYFGRK | VAIDASMSIY | QFLIAVRQGG |
| 60 | 70 | 80 | 90 | 100 |
| DVLQNEEGET | TSHLMGMFYR | TIRMMENGIK | PVYVFDGKPP | QLKSGELAKR |
| 110 | 120 | 130 | 140 | 150 |
| SERRAEAEKQ | LQQAQAAGAE | QEVEKFTKRL | VKVTKQHNDE | CKHLLSLMGI |
| 160 | 170 | 180 | 190 | 200 |
| PYLDAPSEAE | ASCAALVKAG | KVYAAATEDM | DCLTFGSPVL | MRHLTASEAK |
| 210 | 220 | 230 | 240 | 250 |
| KLPIQEFHLS | RILQELGLNQ | EQFVDLCILL | GSDYCESIRG | IGPKRAVDLI |
| 260 | 270 | 280 | 290 | 300 |
| QKHKSIEEIV | RRLDPNKYPV | PENWLHKEAH | QLFLEPEVLD | PESVELKWSE |
| 310 | 320 | 330 | 340 | 350 |
| PNEEELIKFM | CGEKQFSEER | IRSGVKRLSK | SRQGSTQGRL | DDFFKVTGSL |
| 360 | 370 | 380 | ||
| SSAKRKEPEP | KGSTKKKAKT | GAAGKFKRGK |
Data source: UniProt
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-1411 Collapse assay details
Data source: Panorama
Official Gene Symbol
FEN1
Peptide Sequence
LIADVAPSAIR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
9
Peptide End
19
CPTAC ID
CPTAC-1411
Peptide Molecular Mass
1,124.6554
Species
Homo sapiens (Human)
Assay Type
Direct ImmunoMRM
Matrix
depleted digested plasma
Submitting Laboratory
Broad Institute
Submitting Lab PI
Steven A. Carr
Publication
View Details (opens in a new window)
Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18. PMID: 25693799
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Quantiva TSQ
Internal Standard
heavy stable isotope peptide (delta 8-10)
Peptide Standard Purity
>95%
Peptide Standard Label Type
15N
LC
Easy NanoLC1000
Column Packing
Reprosil C18, 1.9um, 200A
Column Dimensions
0.075 x 150 mm
Flow Rate
200 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 |
| y6 (1+) | 6.4 | 1.7 | 1 | 8.5 | 6.7 | 3.4 | 10.6 | 6.9 | 3.5 | 15 | 15 | 15 |
| y9 (1+) | 4.2 | 1.6 | 1.5 | 8.3 | 6.2 | 3.4 | 9.3 | 6.4 | 3.7 | 15 | 15 | 15 |
| y5 (1+) | 4 | 3 | 2.3 | 9.7 | 6.2 | 2.9 | 10.5 | 6.9 | 3.7 | 15 | 15 | 15 |
| sum | 2.7 | 1.3 | 1.1 | 8.4 | 6.1 | 3 | 8.8 | 6.2 | 3.2 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-1410 Collapse assay details
Data source: Panorama
Official Gene Symbol
FEN1
Peptide Sequence
QLQQAQAAGAEQEVEK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
110
Peptide End
125
CPTAC ID
CPTAC-1410
Peptide Molecular Mass
1,726.8486
Species
Homo sapiens (Human)
Assay Type
Direct ImmunoMRM
Matrix
depleted digested plasma
Submitting Laboratory
Broad Institute
Submitting Lab PI
Steven A. Carr
Publication
View Details (opens in a new window)
Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18. PMID: 25693799
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Quantiva TSQ
Internal Standard
heavy stable isotope peptide (delta 8-10)
Peptide Standard Purity
>95%
Peptide Standard Label Type
15N
LC
Easy NanoLC1000
Column Packing
Reprosil C18, 1.9um, 200A
Column Dimensions
0.075 x 150 mm
Flow Rate
200 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 |
| y5 (1+) | 8.9 | 7.8 | 4.5 | 12.1 | 8 | 4.4 | 15 | 11.2 | 6.3 | 15 | 15 | 15 |
| y9 (2+) | 23.5 | 9.6 | 7.4 | 25.3 | 12.5 | 8.5 | 34.5 | 15.8 | 11.3 | 15 | 15 | 15 |
| y6 (1+) | 5.8 | 3.5 | 2.7 | 8.4 | 8.6 | 3 | 10.2 | 9.3 | 4 | 15 | 15 | 15 |
| sum | 9.3 | 4.6 | 3.1 | 8.7 | 7.3 | 3.2 | 12.7 | 8.6 | 4.5 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-1409 Collapse assay details
Data source: Panorama
Official Gene Symbol
FEN1
Peptide Sequence
SIEEIVR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
255
Peptide End
261
CPTAC ID
CPTAC-1409
Peptide Molecular Mass
844.4654
Species
Homo sapiens (Human)
Assay Type
Direct ImmunoMRM
Matrix
depleted digested plasma
Submitting Laboratory
Broad Institute
Submitting Lab PI
Steven A. Carr
Publication
View Details (opens in a new window)
Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18. PMID: 25693799
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Quantiva TSQ
Internal Standard
heavy stable isotope peptide (delta 8-10)
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Easy NanoLC1000
Column Packing
Reprosil C18, 1.9um, 200A
Column Dimensions
0.075 x 150 mm
Flow Rate
200 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 |
| y6 (1+) | 21.1 | 11 | 8.1 | 15.5 | 11.3 | 9.4 | 26.2 | 15.8 | 12.4 | 15 | 15 | 15 |
| y5 (1+) | 3 | 2.8 | 2.9 | 3.3 | 7.2 | 4.3 | 4.5 | 7.7 | 5.2 | 15 | 15 | 15 |
| y4 (1+) | 4.3 | 3.7 | 1.7 | 4 | 7.7 | 3.5 | 5.9 | 8.5 | 3.9 | 15 | 15 | 15 |
| sum | 3 | 2.9 | 2.5 | 3.3 | 7.2 | 4.1 | 4.5 | 7.8 | 4.8 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-700 Collapse assay details
Data source: Panorama
Official Gene Symbol
FEN1
Peptide Sequence
SIEEIVR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
255
Peptide End
261
CPTAC ID
CPTAC-700
Peptide Molecular Mass
844.4654
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
plasma
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
Publication
View Details (opens in a new window)
Anti-peptide monoclonal antibodies generated for immuno-multiple reaction monitoring-mass spectrometry assays have a high probability of supporting Western blot and ELISA. Schoenherr RM, Saul RG, Whiteaker JR, Yan P, Whiteley GR, Paulovich AG. Mol Cell Proteomics. 2015 Feb;14(2):382-98. doi: 10.1074/mcp.O114.043133. Epub 2014 Dec 15. PMID: 25512614
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
5500 Qtrap
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent NanoLC 2D
Column Packing
ReproSil-Pur C18-AQ 3 um
Column Dimensions
100 mm x 75 um ID
Flow Rate
300 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 |
| y3 (1+) | 93.7 | 48.1 | 75 | 109.5 | 52.4 | 66.4 | 144.1 | 71.1 | 100.2 | 15 | 15 | 15 |
| y4 (1+) | 34.4 | 8.4 | 15.1 | 36.4 | 12.7 | 17.2 | 50.1 | 15.2 | 22.9 | 15 | 15 | 15 |
| y5 (1+) | 16.4 | 7.2 | 3.6 | 18.2 | 7.7 | 5.4 | 24.5 | 10.5 | 6.5 | 15 | 15 | 15 |
| sum | 19.8 | 9.6 | 9.5 | 19.9 | 11.9 | 8.2 | 28.1 | 15.3 | 12.5 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-3230 Collapse assay details
Data source: Panorama
Official Gene Symbol
FEN1
Peptide Sequence
SIEEIVR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
255
Peptide End
261
CPTAC ID
CPTAC-3230
Peptide Molecular Mass
844.4654
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
Publication
View Details (opens in a new window)
A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. Radiat Res. 2018 Feb 23. doi: 10.1667/RR14963.1. [Epub ahead of print]
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
6500 QTRAP (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 uL/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 |
| y4 (1+) | 71 | 41.2 | 17.3 | 72.6 | 39.3 | 15.9 | 101.5 | 56.9 | 23.5 | 15 | 15 | 15 |
| y5 (1+) | 39.5 | 10.9 | 9.4 | 56.1 | 16.9 | 14.6 | 68.6 | 20.1 | 17.4 | 15 | 15 | 15 |
| y6 (1+) | 96.5 | 89.8 | 57.1 | 93.2 | 110.8 | 67 | 134.2 | 142.6 | 88 | 15 | 15 | 15 |
| sum | 36.2 | 12.3 | 9.7 | 51.3 | 18.4 | 11.6 | 62.8 | 22.1 | 15.1 | 15 | 15 | 15 |