RB1, CPTAC-898 - CPTAC Assay Portal (original) (raw)
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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.
Protein Sequence hover to view complete sequence
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MPPKTPRKTA | ATAAAAAAEP | PAPPPPPPPE | EDPEQDSGPE | DLPLVRLEFE |
| 60 | 70 | 80 | 90 | 100 |
| ETEEPDFTAL | CQKLKIPDHV | RERAWLTWEK | VSSVDGVLGG | YIQKKKELWG |
| 110 | 120 | 130 | 140 | 150 |
| ICIFIAAVDL | DEMSFTFTEL | QKNIEISVHK | FFNLLKEIDT | STKVDNAMSR |
| 160 | 170 | 180 | 190 | 200 |
| LLKKYDVLFA | LFSKLERTCE | LIYLTQPSSS | ISTEINSALV | LKVSWITFLL |
| 210 | 220 | 230 | 240 | 250 |
| AKGEVLQMED | DLVISFQLML | CVLDYFIKLS | PPMLLKEPYK | TAVIPINGSP |
| 260 | 270 | 280 | 290 | 300 |
| RTPRRGQNRS | ARIAKQLEND | TRIIEVLCKE | HECNIDEVKN | VYFKNFIPFM |
| 310 | 320 | 330 | 340 | 350 |
| NSLGLVTSNG | LPEVENLSKR | YEEIYLKNKD | LDARLFLDHD | KTLQTDSIDS |
| 360 | 370 | 380 | 390 | 400 |
| FETQRTPRKS | NLDEEVNVIP | PHTPVRTVMN | TIQQLMMILN | SASDQPSENL |
| 410 | 420 | 430 | 440 | 450 |
| ISYFNNCTVN | PKESILKRVK | DIGYIFKEKF | AKAVGQGCVE | IGSQRYKLGV |
| 460 | 470 | 480 | 490 | 500 |
| RLYYRVMESM | LKSEEERLSI | QNFSKLLNDN | IFHMSLLACA | LEVVMATYSR |
| 510 | 520 | 530 | 540 | 550 |
| STSQNLDSGT | DLSFPWILNV | LNLKAFDFYK | VIESFIKAEG | NLTREMIKHL |
| 560 | 570 | 580 | 590 | 600 |
| ERCEHRIMES | LAWLSDSPLF | DLIKQSKDRE | GPTDHLESAC | PLNLPLQNNH |
| 610 | 620 | 630 | 640 | 650 |
| TAADMYLSPV | RSPKKKGSTT | RVNSTANAET | QATSAFQTQK | PLKSTSLSLF |
| 660 | 670 | 680 | 690 | 700 |
| YKKVYRLAYL | RLNTLCERLL | SEHPELEHII | WTLFQHTLQN | EYELMRDRHL |
| 710 | 720 | 730 | 740 | 750 |
| DQIMMCSMYG | ICKVKNIDLK | FKIIVTAYKD | LPHAVQETFK | RVLIKEEEYD |
| 760 | 770 | 780 | 790 | 800 |
| SIIVFYNSVF | MQRLKTNILQ | YASTRPPTLS | PIPHIPRSPY | KFPSSPLRIP |
| 810 | 820 | 830 | 840 | 850 |
| GGNIYISPLK | SPYKISEGLP | TPTKMTPRSR | ILVSIGESFG | TSEKFQKINQ |
| 860 | 870 | 880 | 890 | 900 |
| MVCNSDRVLK | RSAEGSNPPK | PLKKLRFDIE | GSDEADGSKH | LPGESKFQQK |
| 910 | 920 | 928 | ||
| LAEMTSTRTR | MQKQKMNDSM | DTSNKEEK |
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-1328 Collapse assay details
Data source: Panorama
Official Gene Symbol
RB1
Peptide Modified Sequence
TAVIPINGS[+80.0]PR
Modification Type
Phospho (ST)
Protein - Site of Modification
249
Peptide - Site of Modification
9
Peptide Start
241
Peptide End
251
CPTAC ID
CPTAC-1328
Peptide Molecular Mass
1,203.6013
Species
Homo sapiens (Human)
Assay Type
Enrichment PRM
Enrichment Method
N/A
Matrix
Digested Cell Lysate
Submitting Laboratory
Broad Institute
Submitting Lab PI
Steven A. Carr
Publication
View Details (opens in a new window)
Abelin, et al. Mol Cell Proteomics. 2016 May;15(5):1622-41. doi: 10.1074/mcp.M116.058354. Epub 2016 Feb 24. PMID:26912667
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Quantiva TSQ
Internal Standard
medium stable isotope peptide (delta 6 amu)
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Easy NanoLC1000
Column Packing
Reprosil C18, 3 um, 200A
Column Dimensions
0.075 x 100 mm
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 |
| y8 (1+) | 10.5 | 4.9 | 4.9 | 11.9 | 8.7 | 13.3 | 15.9 | 10 | 14.2 | 15 | 15 | 15 |
| y7 (1+) | 5.2 | 2.9 | 3.3 | 7.6 | 4.1 | 8.5 | 9.2 | 5 | 9.1 | 15 | 15 | 15 |
| y7-98 (1+) | 5.7 | 4.7 | 7.4 | 6.3 | 7.6 | 13.5 | 8.5 | 8.9 | 15.4 | 15 | 15 | 15 |
| sum | 4.7 | 2.9 | 3.6 | 5.9 | 4.7 | 9.7 | 7.5 | 5.5 | 10.3 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-942 Collapse assay details
Data source: Panorama
Official Gene Symbol
RB1
Peptide Modified Sequence
IPGGNIYIS[+80.0]PLK
Modification Type
Phospho (ST)
Protein - Site of Modification
807
Peptide - Site of Modification
9
Peptide Start
799
Peptide End
810
CPTAC ID
CPTAC-942
Peptide Molecular Mass
1,350.6949
Species
Homo sapiens (Human)
Assay Type
Enrichment PRM
Enrichment Method
N/A
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 K
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
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 (2+) | 51.1 | 30.6 | 47.9 | 41.2 | 25.3 | 34.9 | 65.6 | 39.7 | 59.3 | 15 | 24 | 15 |
| y11 (2+) | 50.3 | 15.7 | 16.4 | 40.4 | 12.9 | 17.1 | 64.5 | 20.3 | 23.7 | 15 | 24 | 15 |
| y6 (1+) | 46.2 | 33.1 | 45.2 | 48.9 | 36.1 | 73 | 67.3 | 49 | 85.9 | 15 | 24 | 15 |
| sum | 40.5 | 15.3 | 21 | 36.9 | 11.9 | 20.8 | 54.8 | 19.4 | 29.6 | 15 | 24 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-3251 Collapse assay details
Data source: Panorama
Official Gene Symbol
RB1
Peptide Sequence
IPGGNIYISPLK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
799
Peptide End
810
CPTAC ID
CPTAC-3251
Peptide Molecular Mass
1,270.7285
Species
Homo sapiens (Human)
Assay Type
Enrichment PRM
Enrichment Method
N/A
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 K
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 |
| y3 (1+) | 14.9 | 12.4 | 10.3 | 18.4 | 14.3 | 12.5 | 23.7 | 18.9 | 16.2 | 15 | 15 | 15 |
| y6 (1+) | 24 | 12.1 | 5.8 | 22.2 | 13 | 7.3 | 32.7 | 17.8 | 9.3 | 15 | 15 | 15 |
| y5 (1+) | 26.4 | 18.6 | 16.4 | 36.5 | 18.1 | 18.9 | 45 | 26 | 25 | 15 | 15 | 15 |
| sum | 10 | 11 | 6 | 13.2 | 9.8 | 8.6 | 16.6 | 14.7 | 10.5 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-3288 Collapse assay details
Data source: Panorama
Official Gene Symbol
RB1
Peptide Modified Sequence
IPGGNIYIS[+80.0]PLK
Modification Type
Phospho (ST)
Protein - Site of Modification
807
Peptide - Site of Modification
9
Peptide Start
799
Peptide End
810
CPTAC ID
CPTAC-3288
Peptide Molecular Mass
1,350.6949
Species
Homo sapiens (Human)
Assay Type
Enrichment PRM
Enrichment Method
N/A
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 K
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 |
| y5 (1+) | 63.2 | 45.5 | 54.1 | 91.1 | 51.7 | 76.7 | 110.9 | 68.9 | 93.9 | 15 | 15 | 15 |
| y6 (1+) | 55.9 | 12.9 | 26.5 | 52.8 | 21.5 | 23.7 | 76.9 | 25.1 | 35.6 | 15 | 15 | 15 |
| y10 (1+) | 31.5 | 48.1 | 5.9 | 47 | 88.4 | 13.1 | 56.6 | 100.6 | 14.4 | 15 | 15 | 15 |
| y10 (2+) | 26.4 | 38.8 | 27.1 | 40 | 37.6 | 32.7 | 47.9 | 54 | 42.5 | 15 | 15 | 15 |
| y3 (1+) | 37.8 | 30.1 | 12.6 | 53.1 | 36.4 | 21.6 | 65.2 | 47.2 | 25 | 15 | 15 | 15 |
| sum | 19.1 | 12.7 | 9.3 | 33.6 | 18.1 | 12.3 | 38.6 | 22.1 | 15.4 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-941 Collapse assay details
Data source: Panorama
Official Gene Symbol
RB1
Peptide Modified Sequence
TAVIPINGS[+80.0]PR
Modification Type
Phospho (ST)
Protein - Site of Modification
249
Peptide - Site of Modification
9
Peptide Start
241
Peptide End
251
CPTAC ID
CPTAC-941
Peptide Molecular Mass
1,203.6013
Species
Homo sapiens (Human)
Assay Type
Enrichment PRM
Enrichment Method
N/A
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
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 |
| y7 (2+) | 19.7 | 5.9 | 9.9 | 27.5 | 6.8 | 9.9 | 33.8 | 9 | 14 | 15 | 24 | 15 |
| y6 (1+) | 18.7 | 9.4 | 9.9 | 32.8 | 12.6 | 13.3 | 37.8 | 15.7 | 16.6 | 15 | 24 | 15 |
| y7 (1+) | 15.6 | 6.5 | 4.8 | 27.1 | 8.5 | 5.8 | 31.3 | 10.7 | 7.5 | 15 | 24 | 15 |
| sum | 15.6 | 5.7 | 4.8 | 26.5 | 7.8 | 5.8 | 30.8 | 9.7 | 7.5 | 15 | 24 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-898 Collapse assay details
Data source: Panorama
Official Gene Symbol
RB1
Peptide Modified Sequence
IPGGNIYIS[+80.0]PLK
Modification Type
Phospho (ST)
Protein - Site of Modification
807
Peptide - Site of Modification
9
Peptide Start
799
Peptide End
810
CPTAC ID
CPTAC-898
Peptide Molecular Mass
1,350.6949
Species
Homo sapiens (Human)
Assay Type
Direct PRM
Matrix
Pooled patient derived xenograft breast tumor digest
Submitting Laboratory
Washington University in St. Louis
Submitting Lab PI
Reid Townsend
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
TripleTOF 5600+ (SCIEX)
Internal Standard
Peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
2DPlus nano-LC (Eksigent)
Column Packing
ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions
200 µm x 15 cm
Flow Rate
800 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 |
| y4 (1+) | 43.6 | 26.7 | 10.8 | 44.5 | 26.2 | 11.4 | 62.3 | 37.4 | 15.7 | 15 | 15 | 15 |
| b6 (1+) | 36.7 | 29.9 | 18.8 | 43.8 | 28.5 | 19.6 | 57.1 | 41.3 | 27.2 | 15 | 15 | 15 |
| b5 (1+) | 24.3 | 10.6 | 11.2 | 23.8 | 12.8 | 10 | 34 | 16.6 | 15 | 15 | 15 | 15 |
| sum | 20.3 | 12.5 | 8.7 | 22.2 | 13.4 | 7.6 | 30.1 | 18.3 | 11.6 | 15 | 15 | 15 |