TF, CPTAC-1157 - 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
non-CPTAC-1157: View additional DGAGDVAFVK data
non-CPTAC-1159: View additional EFQLFSSPHGK data
non-CPTAC-3439: View additional HQTVLDNTEGK data
non-CPTAC-5621: View additional IPSHAVVAR data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MRLAVGALLV | CAVLGLCLAV | PDKTVRWCAV | SEHEATKCQS | FRDHMKSVIP |
| 60 | 70 | 80 | 90 | 100 |
| SDGPSVACVK | KASYLDCIRA | IAANEADAVT | LDAGLVYDAY | LAPNNLKPVV |
| 110 | 120 | 130 | 140 | 150 |
| AEFYGSKEDP | QTFYYAVAVV | KKDSGFQMNQ | LRGKKSCHTG | LGRSAGWNIP |
| 160 | 170 | 180 | 190 | 200 |
| IGLLYCDLPE | PRKPLEKAVA | NFFSGSCAPC | ADGTDFPQLC | QLCPGCGCST |
| 210 | 220 | 230 | 240 | 250 |
| LNQYFGYSGA | FKCLKDGAGD | VAFVKHSTIF | ENLANKADRD | QYELLCLDNT |
| 260 | 270 | 280 | 290 | 300 |
| RKPVDEYKDC | HLAQVPSHTV | VARSMGGKED | LIWELLNQAQ | EHFGKDKSKE |
| 310 | 320 | 330 | 340 | 350 |
| FQLFSSPHGK | DLLFKDSAHG | FLKVPPRMDA | KMYLGYEYVT | AIRNLREGTC |
| 360 | 370 | 380 | 390 | 400 |
| PEAPTDECKP | VKWCALSHHE | RLKCDEWSVN | SVGKIECVSA | ETTEDCIAKI |
| 410 | 420 | 430 | 440 | 450 |
| MNGEADAMSL | DGGFVYIAGK | CGLVPVLAEN | YNKSDNCEDT | PEAGYFAIAV |
| 460 | 470 | 480 | 490 | 500 |
| VKKSASDLTW | DNLKGKKSCH | TAVGRTAGWN | IPMGLLYNKI | NHCRFDEFFS |
| 510 | 520 | 530 | 540 | 550 |
| EGCAPGSKKD | SSLCKLCMGS | GLNLCEPNNK | EGYYGYTGAF | RCLVEKGDVA |
| 560 | 570 | 580 | 590 | 600 |
| FVKHQTVPQN | TGGKNPDPWA | KNLNEKDYEL | LCLDGTRKPV | EEYANCHLAR |
| 610 | 620 | 630 | 640 | 650 |
| APNHAVVTRK | DKEACVHKIL | RQQQHLFGSN | VTDCSGNFCL | FRSETKDLLF |
| 660 | 670 | 680 | 690 | 698 |
| RDDTVCLAKL | HDRNTYEKYL | GEEYVKAVGN | LRKCSTSSLL | EACTFRRP |
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 non-CPTAC-1157 Collapse assay details
Data source: Panorama
Official Gene Symbol
TF
Peptide Sequence
DGAGDVAFVK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
216
Peptide End
225
CPTAC ID
non-CPTAC-1157
Peptide Molecular Mass
977.4818
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
6490 Triple Quad (Agilent)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/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 |
| b3 (1+) | 6 | 6.6 | 6 | 10.8 | 8.7 | 6.4 | 12.4 | 10.9 | 8.8 | 15 | 15 | 15 |
| y8 (2+) | 8.6 | 6.6 | 4.7 | 12.8 | 7.2 | 3.2 | 15.4 | 9.8 | 5.7 | 15 | 15 | 15 |
| y4 (1+) | 8.3 | 5.7 | 5.7 | 11.9 | 9.6 | 6 | 14.5 | 11.2 | 8.3 | 15 | 15 | 15 |
| y5 (1+) | 9.6 | 6.7 | 6.6 | 16 | 9.8 | 5.9 | 18.7 | 11.9 | 8.9 | 15 | 15 | 15 |
| y7 (1+) | 7.5 | 5.7 | 5.6 | 9.4 | 9.5 | 8.1 | 12 | 11.1 | 9.8 | 15 | 15 | 15 |
| sum | 3.7 | 3.9 | 3.4 | 8.7 | 7 | 4.4 | 9.5 | 8 | 5.6 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-1159 Collapse assay details
Data source: Panorama
Official Gene Symbol
TF
Peptide Sequence
EFQLFSSPHGK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
300
Peptide End
310
CPTAC ID
non-CPTAC-1159
Peptide Molecular Mass
1,275.6248
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
6490 Triple Quad (Agilent)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/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 (2+) | 5.1 | 4.1 | 3.9 | 12.3 | 5 | 4 | 13.3 | 6.5 | 5.6 | 15 | 15 | 15 |
| y9 (2+) | 7.1 | 6 | 4.3 | 14 | 9.9 | 4.8 | 15.7 | 11.6 | 6.4 | 15 | 15 | 15 |
| y3 (1+) | 8.8 | 6 | 4.8 | 14.2 | 10.1 | 5.1 | 16.7 | 11.7 | 7 | 15 | 15 | 15 |
| y4 (1+) | 6 | 7.2 | 4.6 | 11.4 | 8.8 | 5 | 12.9 | 11.4 | 6.8 | 15 | 15 | 15 |
| y6 (1+) | 5.1 | 5.6 | 4.6 | 11.9 | 9.3 | 5.4 | 12.9 | 10.9 | 7.1 | 15 | 15 | 15 |
| sum | 3.3 | 2.8 | 2.8 | 11.3 | 5.3 | 2.9 | 11.8 | 6 | 4 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-3439 Collapse assay details
Data source: Panorama
Official Gene Symbol
Tf
Peptide Sequence
HQTVLDNTEGK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
555
Peptide End
565
CPTAC ID
non-CPTAC-3439
Peptide Molecular Mass
1,240.6048
Species
Mus musculus (Mouse)
Assay Type
Direct MRM
Matrix
Plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Publication
View Details (opens in a new window)
Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays. Michaud SA, Sinclair NJ, Petrošová H, Palmer AL, Pistawka AJ, Zhang S, Hardie DB, Mohammed Y Eshghi A1, Richard VR, Sickmann A, Borchers CH. Commun Biol. 2018 Jun 27;1:78. doi: 10.1038/s42003-018-0087-6. eCollection 2018.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Agilent 6490/6495 QQQ
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/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 |
| b4 (1+) | 5.3 | 7 | 6.2 | 16.9 | 13.7 | 9.4 | 17.7 | 15.4 | 11.3 | 15 | 15 | 15 |
| b3 (1+) | 6 | 6.6 | 8.1 | 12.9 | 7.3 | 9.2 | 14.2 | 9.8 | 12.3 | 15 | 15 | 15 |
| b2 (1+) | 5.8 | 6.6 | 5.2 | 14.9 | 8 | 7.7 | 16 | 10.4 | 9.3 | 15 | 15 | 15 |
| y2 (1+) | 5.5 | 8.8 | 9.3 | 14 | 9.9 | 10.2 | 15 | 13.2 | 13.8 | 15 | 15 | 15 |
| y6 (1+) | 3.5 | 8.1 | 7.8 | 14.5 | 7.6 | 8.2 | 14.9 | 11.1 | 11.3 | 15 | 15 | 15 |
| sum | 2.9 | 3.2 | 3.2 | 14.4 | 7 | 5.8 | 14.7 | 7.7 | 6.6 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-5621 Collapse assay details
Data source: Panorama
Official Gene Symbol
Tf
Peptide Sequence
IPSHAVVAR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
265
Peptide End
273
CPTAC ID
non-CPTAC-5621
Peptide Molecular Mass
948.5505
Species
Mus musculus (Mouse)
Assay Type
Direct MRM
Matrix
Plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Agilent 6490/6495 QQQ
Internal Standard
synthetic peptide
Peptide Standard Purity
>80%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/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 (2+) | 7.3 | 3.8 | 6.9 | 9.1 | 6.1 | 6.6 | 11.7 | 7.2 | 9.5 | 15 | 15 | 15 |
| y7 (2+) | 17 | 3.3 | 2.8 | 17.8 | 6.8 | 3.8 | 24.6 | 7.6 | 4.7 | 15 | 15 | 15 |
| y8 (2+) | 6.4 | 2.3 | 2.3 | 9.3 | 6.8 | 5.9 | 11.3 | 7.2 | 6.3 | 15 | 15 | 15 |
| y4 (1+) | 17.2 | 3.9 | 4 | 16.5 | 7.7 | 5.1 | 23.8 | 8.6 | 6.5 | 15 | 15 | 15 |
| y5 (1+) | 6.5 | 2.8 | 4 | 8.3 | 5.2 | 4.5 | 10.5 | 5.9 | 6 | 15 | 15 | 15 |
| sum | 3.5 | 1.4 | 1.8 | 5.3 | 5.5 | 3.3 | 6.4 | 5.7 | 3.8 | 15 | 15 | 15 |