RAD50, CPTAC-954 - 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

10 20 30 40 50
MSRIEKMSIL GVRSFGIEDK DKQIITFFSP LTILVGPNGA GKTTIIECLK
60 70 80 90 100
YICTGDFPPG TKGNTFVHDP KVAQETDVRA QIRLQFRDVN GELIAVQRSM
110 120 130 140 150
VCTQKSKKTE FKTLEGVITR TKHGEKVSLS SKCAEIDREM ISSLGVSKAV
160 170 180 190 200
LNNVIFCHQE DSNWPLSEGK ALKQKFDEIF SATRYIKALE TLRQVRQTQG
210 220 230 240 250
QKVKEYQMEL KYLKQYKEKA CEIRDQITSK EAQLTSSKEI VKSYENELDP
260 270 280 290 300
LKNRLKEIEH NLSKIMKLDN EIKALDSRKK QMEKDNSELE EKMEKVFQGT
310 320 330 340 350
DEQLNDLYHN HQRTVREKER KLVDCHRELE KLNKESRLLN QEKSELLVEQ
360 370 380 390 400
GRLQLQADRH QEHIRARDSL IQSLATQLEL DGFERGPFSE RQIKNFHKLV
410 420 430 440 450
RERQEGEAKT ANQLMNDFAE KETLKQKQID EIRDKKTGLG RIIELKSEIL
460 470 480 490 500
SKKQNELKNV KYELQQLEGS SDRILELDQE LIKAERELSK AEKNSNVETL
510 520 530 540 550
KMEVISLQNE KADLDRTLRK LDQEMEQLNH HTTTRTQMEM LTKDKADKDE
560 570 580 590 600
QIRKIKSRHS DELTSLLGYF PNKKQLEDWL HSKSKEINQT RDRLAKLNKE
610 620 630 640 650
LASSEQNKNH INNELKRKEE QLSSYEDKLF DVCGSQDFES DLDRLKEEIE
660 670 680 690 700
KSSKQRAMLA GATAVYSQFI TQLTDENQSC CPVCQRVFQT EAELQEVISD
710 720 730 740 750
LQSKLRLAPD KLKSTESELK KKEKRRDEML GLVPMRQSII DLKEKEIPEL
760 770 780 790 800
RNKLQNVNRD IQRLKNDIEE QETLLGTIMP EEESAKVCLT DVTIMERFQM
810 820 830 840 850
ELKDVERKIA QQAAKLQGID LDRTVQQVNQ EKQEKQHKLD TVSSKIELNR
860 870 880 890 900
KLIQDQQEQI QHLKSTTNEL KSEKLQISTN LQRRQQLEEQ TVELSTEVQS
910 920 930 940 950
LYREIKDAKE QVSPLETTLE KFQQEKEELI NKKNTSNKIA QDKLNDIKEK
960 970 980 990 1000
VKNIHGYMKD IENYIQDGKD DYKKQKETEL NKVIAQLSEC EKHKEKINED
1010 1020 1030 1040 1050
MRLMRQDIDT QKIQERWLQD NLTLRKRNEE LKEVEEERKQ HLKEMGQMQV
1060 1070 1080 1090 1100
LQMKSEHQKL EENIDNIKRN HNLALGRQKG YEEEIIHFKK ELREPQFRDA
1110 1120 1130 1140 1150
EEKYREMMIV MRTTELVNKD LDIYYKTLDQ AIMKFHSMKM EEINKIIRDL
1160 1170 1180 1190 1200
WRSTYRGQDI EYIEIRSDAD ENVSASDKRR NYNYRVVMLK GDTALDMRGR
1210 1220 1230 1240 1250
CSAGQKVLAS LIIRLALAET FCLNCGIIAL DEPTTNLDRE NIESLAHALV
1260 1270 1280 1290 1300
EIIKSRSQQR NFQLLVITHD EDFVELLGRS EYVEKFYRIK KNIDQCSEIV
1310 1312
KCSVSSLGFN VH

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


Phosphorylation Acetylation Ubiquitylation Other

loading

Loader


Assay Details for CPTAC-954 Collapse assay details

Data source: Panorama

Official Gene Symbol

RAD50

Peptide Modified Sequence

LFDVC[+57.0]GS[+80.0]QDFESDLDR

Modification Type

Carbamidomethyl Cysteine, Phospho (ST)

Protein - Site of Modification

633, 635

Peptide - Site of Modification

5, 7

Peptide Start

629

Peptide End

644

CPTAC ID

CPTAC-954

Peptide Molecular Mass

1,981.7765

Species

Homo sapiens (Human)

Assay Type

Enrichment MRM

Enrichment Method

IMAC

Matrix

cell lysate

Submitting Laboratory

Fred Hutchinson Cancer Research Center

Submitting Lab PI

Amanda Paulovich


Publication

View Details (opens in a new window)

Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich U, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG. Immobilized metal affinity chromatography coupled to multiple reaction monitoring enables reproducible quantification of phospho-signaling. Molecular and Cellular Proteomics. mcp.O115.054940


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

QTrap 5500 (Sciex)

Internal Standard

Peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

nanoLC-2D (Eksigent)

Column Packing

ChromXP C18-CL, 3 µm, 120 Å

Column Dimensions

75 µm x 15cm

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 CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y5 (1+) | 57.8 | 9.8 | 10.4 | 59.5 | 36.9 | 15.9 | 83 | 38.2 | 19 | 13 | 24 | 15 | | y6 (1+) | 32.4 | 10.8 | 10.6 | 40.1 | 37.6 | 19.3 | 51.6 | 39.1 | 22 | 13 | 24 | 15 | | y7 (1+) | 35.5 | 13.2 | 11.7 | 42.4 | 47.4 | 14.1 | 55.3 | 49.2 | 18.3 | 13 | 24 | 15 | | sum | 27.6 | 8.4 | 10 | 32.5 | 38.6 | 16.2 | 42.6 | 39.5 | 19 | 13 | 24 | 15 |



Additional Resources and Comments


Assay Details for CPTAC-3286 Collapse assay details

Data source: Panorama

Official Gene Symbol

RAD50

Peptide Modified Sequence

LFDVC[+57.0]GSQDFESDLDR

Modification Type

Carbamidomethyl Cysteine

Protein - Site of Modification

633

Peptide - Site of Modification

5

Peptide Start

629

Peptide End

644

CPTAC ID

CPTAC-3286

Peptide Molecular Mass

1,901.8102

Species

Homo sapiens (Human)

Assay Type

Enrichment MRM

Enrichment Method

IMAC

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

Loader


Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y8 (1+) | 35 | 28.7 | 31.2 | 41.6 | 27 | 31.6 | 54.4 | 39.4 | 44.4 | 15 | 15 | 15 | | y10 (1+) | 43.3 | 17.5 | 33.2 | 49.3 | 21.6 | 34.7 | 65.6 | 27.8 | 48 | 15 | 15 | 15 | | y6 (1+) | 41.2 | 32.1 | 31.6 | 46 | 38.9 | 39.9 | 61.8 | 50.4 | 50.9 | 15 | 15 | 15 | | y7 (1+) | 27.2 | 16.8 | 27.5 | 54.9 | 22.9 | 33.5 | 61.3 | 28.4 | 43.3 | 15 | 15 | 15 | | sum | 29.9 | 20.8 | 29.1 | 40.6 | 20.7 | 33.1 | 50.4 | 29.3 | 44.1 | 15 | 15 | 15 |



Additional Resources and Comments


Assay Details for CPTAC-5927 Collapse assay details

Data source: Panorama

Official Gene Symbol

RAD50

Peptide Modified Sequence

YELQQLEGS[+79.966331]SDR

Modification Type

Phospho (ST)

Protein - Site of Modification

471

Peptide - Site of Modification

9

Peptide Start

462

Peptide End

473

CPTAC ID

CPTAC-5927

Peptide Molecular Mass

1,503.6243

Species

Homo sapiens (Human)

Assay Type

Enrichment MRM

Enrichment Method

IMAC

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 R

LC

Eksigent 425

Column Packing

Reprosil

Column Dimensions

75um x 15cm

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 CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y10 (2+) | 30.2 | 16.9 | 11.4 | 53.4 | 18.3 | 14.2 | 61.3 | 24.9 | 18.2 | 15 | 27 | 15 | | b6 (1+) | 44.7 | 24.5 | 10 | 58.4 | 25.3 | 14.1 | 73.5 | 35.2 | 17.3 | 15 | 27 | 15 | | y7 (1+) | 28.9 | 18.4 | 11 | 32.7 | 30.6 | 18.8 | 43.6 | 35.7 | 21.8 | 15 | 27 | 15 | | y6 (1+) | 49.6 | 17.7 | 8.7 | 49.4 | 19.2 | 19.6 | 70 | 26.1 | 21.4 | 15 | 27 | 15 | | y6-98 (1+) | 40.3 | 15.4 | 9.5 | 40.5 | 27.3 | 13.1 | 57.1 | 31.3 | 16.2 | 15 | 27 | 15 | | y5 (1+) | 60 | 20.3 | 12.7 | 59.6 | 22.2 | 17.9 | 84.6 | 30.1 | 21.9 | 15 | 27 | 15 | | y5-98 (1+) | 33.5 | 10.8 | 6.3 | 44.2 | 15.7 | 15.2 | 55.5 | 19.1 | 16.5 | 15 | 27 | 15 | | sum | 17.4 | 9.1 | 4.7 | 17.2 | 12.6 | 13.1 | 24.5 | 15.5 | 13.9 | 15 | 27 | 15 |



Additional Resources and Comments