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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.

RTF1

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
RTF1 KIAA0252
Sequence Length (AA) Molecular Weight (Da)
710 80313
Protein Name
RNA polymerase-associated protein RTF1 homolog
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MRGRLCVGRA AAAAAAVAVP LAGGQEGSPG GGRRGSRGTT MVKKRKGRVV
60 70 80 90 100
IDSDTEDSGS DENLDQELLS LAKRKRSDSE EKEPPVSQPA ASSDSETSDS
110 120 130 140 150
DDEWTFGSNK NKKKGKARKI EKKGTMKKQA NKTASSGSSD KDSSAESSAP
160 170 180 190 200
EEGEVSDSDS NSSSSSSDSD SSSEDEEFHD GYGEDLMGDE EDRARLEQMT
210 220 230 240 250
EKEREQELFN RIEKREVLKR RFEIKKKLKT AKKKEKKEKK KKQEEEQEKK
260 270 280 290 300
KLTQIQESQV TSHNKERRSK RDEKLDKKSQ AMEELKAERE KRKNRTAELL
310 320 330 340 350
AKKQPLKTSE VYSDDEEEEE DDKSSEKSDR SSRTSSSDEE EEKEEIPPKS
360 370 380 390 400
QPVSLPEELN RVRLSRHKLE RWCHMPFFAK TVTGCFVRIG IGNHNSKPVY
410 420 430 440 450
RVAEITGVVE TAKVYQLGGT RTNKGLQLRH GNDQRVFRLE FVSNQEFTES
460 470 480 490 500
EFMKWKEAMF SAGMQLPTLD EINKKELSIK EALNYKFNDQ DIEEIVKEKE
510 520 530 540 550
RFRKAPPNYA MKKTQLLKEK AMAEDLGDQD KAKQIQDQLN ELEERAEALD
560 570 580 590 600
RQRTKNISAI SYINQRNREW NIVESEKALV AESHNMKNQQ MDPFTRRQCK
610 620 630 640 650
PTIVSNSRDP AVQAAILAQL NAKYGSGVLP DAPKEMSKGQ GKDKDLNSKS
660 670 680 690 700
ASDLSEDLFK VHDFDVKIDL QVPSSESKAL AITSKAPPAK DGAPRRSLNL
710
EDYKKRRGLI

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-5925 Collapse assay details

Data source: Panorama

Official Gene Symbol
RTF1
Peptide Sequence
SASDLSEDLFK
Modification Type
unmodified
Protein - Site of Modification
650
Peptide - Site of Modification
N/A
Peptide Start
650
Peptide End
660
CPTAC ID
CPTAC-5925
Peptide Molecular Mass
1,210.5717
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)

Targeted Mass Spectrometry Enables Quantification of Novel Pharmacodynamic Biomarkers of ATM Kinase Inhibition. Whiteaker JR, Wang T, Zhao L, Schoenherr RM, Kennedy JJ, Voytovich U, Ivey RG, Huang D, Lin C, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Kaczmarczyk JA, Blonder J, Reading JJ, Richardson CW, Hewitt SM, Garcia-Buntley SS, Bocik W, Hiltke T, Rodriguez H, Harrington EA, Barrett JC, Lombardi B, Marco-Casanova P, Pierce AJ, Paulovich AG. Cancers (Basel). 2021 Jul 30;13(15):3843. doi: 10.3390/cancers13153843. PMID: 34359745

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
Sciex 5500 QTRAP
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent 425
Column Packing
Reprosil
Column Dimensions
75um x 15cm
Flow Rate
300 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
y5 (1+) 23.4 7.6 6.7 29.3 13.7 8.2 37.5 15.7 10.6 15 27 15
y7 (1+) 14.4 7.3 6.9 16.5 12.9 6.7 21.9 14.8 9.6 15 27 15
y9 (1+) 12.1 11.5 7.2 16.3 15.9 7.5 20.3 19.6 10.4 15 27 15
y8 (1+) 18 10.5 5.1 25.8 14.9 7.6 31.5 18.2 9.2 15 27 15
y6 (1+) 8.8 7.2 5.5 13.8 13.4 6 16.4 15.2 8.1 15 27 15
b4 (1+) 20.6 11.6 5.8 29.2 18.1 7.4 35.7 21.5 9.4 15 27 15
b5 (1+) 18.9 9.9 5.8 19.4 14.1 6.6 27.1 17.2 8.8 15 27 15
sum 4.8 5 4.5 10.3 12.5 5.6 11.4 13.5 7.2 15 27 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
View in CPTC Antibody Portal
Comments

Assay Details for CPTAC-5926 Collapse assay details

Data source: Panorama

Official Gene Symbol
RTF1
Peptide Modified Sequence
SASDLS[+79.966331]EDLFK
Modification Type
Phospho (ST)
Protein - Site of Modification
656
Peptide - Site of Modification
6
Peptide Start
650
Peptide End
660
CPTAC ID
CPTAC-5926
Peptide Molecular Mass
1,290.5381
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)

Targeted Mass Spectrometry Enables Quantification of Novel Pharmacodynamic Biomarkers of ATM Kinase Inhibition. Whiteaker JR, Wang T, Zhao L, Schoenherr RM, Kennedy JJ, Voytovich U, Ivey RG, Huang D, Lin C, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Kaczmarczyk JA, Blonder J, Reading JJ, Richardson CW, Hewitt SM, Garcia-Buntley SS, Bocik W, Hiltke T, Rodriguez H, Harrington EA, Barrett JC, Lombardi B, Marco-Casanova P, Pierce AJ, Paulovich AG. Cancers (Basel). 2021 Jul 30;13(15):3843. doi: 10.3390/cancers13153843. PMID: 34359745

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
Sciex 5500 QTRAP
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent 425
Column Packing
Reprosil
Column Dimensions
75um x 15cm
Flow Rate
300 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+) 18.2 14 11.3 21.1 16.1 11.1 27.9 21.3 15.8 15 27 15
y8 (1+) 30.3 13.1 8.6 39.7 11.7 13.6 49.9 17.6 16.1 15 27 15
y7 (1+) 54.5 20.9 14.3 33.9 20.5 15.8 64.2 29.3 21.3 15 27 15
y6 (1+) 10.7 9.4 9.1 23 15.4 12 25.4 18 15.1 15 27 15
y4 (1+) 39.8 11.4 6.6 40.1 15 8.2 56.5 18.8 10.5 15 27 15
y9 (2+) 25.2 10.1 6.6 27.5 15.1 12 37.3 18.2 13.7 15 27 15
y9-98 (2+) 20.4 8.8 10.6 22.5 16 13.2 30.4 18.3 16.9 15 27 15
sum 15.5 5.7 5.1 15.8 11.8 9.8 22.1 13.1 11 15 27 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
View in CPTC Antibody Portal
Comments