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Overview Data source: UniProt

Official Gene Symbol Other Aliases
FEN1 RAD2
Sequence Length (AA) Molecular Weight (Da)
380 42593
Protein Name
Flap endonuclease 1
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

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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All other points link out to UniProt



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 MRM
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

Loader

Repeatability

Data source: Panorama

  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
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 MRM
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

Loader

Repeatability

Data source: Panorama

  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
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 MRM
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

Loader

Repeatability

Data source: Panorama

  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
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 MRM
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

Loader

Repeatability

Data source: Panorama

  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
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 MRM
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]

View Details (opens in a new window)

Targeted mass spectrometry enables robust quantification of FANCD2 mono-ubiquitination in response to DNA damage. Whiteaker JR, Zhao L, Ivey RG, Sanchez-Bonilla M, Moore HD, Schoenherr RM, Yan P, Lin C, Shimamura A, Paulovich AG. DNA Repair (Amst). 2018 May;65:47-53. doi: 10.1016/j.dnarep.2018.03.003. Epub 2018 Mar 21.

View Details (opens in a new window)

Targeted mass spectrometry enables robust quantification of FANCD2 mono-ubiquitination in response to DNA damage. Whiteaker JR, Zhao L, Ivey RG, Sanchez-Bonilla M, Moore HD, Schoenherr RM, Yan P, Lin C, Shimamura A, Paulovich AG. DNA Repair (Amst). 2018 May;65:47-53. doi: 10.1016/j.dnarep.2018.03.003. Epub 2018 Mar 21.

View Details (opens in a new window)

None


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

Loader

Repeatability

Data source: Panorama

  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
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

Additional Resources and Comments