Tgfb1, CPTAC-3952 - 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

CPTAC-6209: View additional EAVPEPVLLSR data

non-CPTAC-3952: View additional LHVEINGISPK data

10 20 30 40 50
MPPSGLRLLP LLLPLPWLLV LTPGRPAAGL STCKTIDMEL VKRKRIEAIR
60 70 80 90 100
GQILSKLRLA SPPSQGEVPP GPLPEAVLAL YNSTRDRVAG ESADPEPEPE
110 120 130 140 150
ADYYAKEVTR VLMVDRNNAI YEKTKDISHS IYMFFNTSDI REAVPEPPLL
160 170 180 190 200
SRAELRLQRL KSSVEQHVEL YQKYSNNSWR YLGNRLLTPT DTPEWLSFDV
210 220 230 240 250
TGVVRQWLNQ GDGIQGFRFS AHCSCDSKDN KLHVEINGIS PKRRGDLGTI
260 270 280 290 300
HDMNRPFLLL MATPLERAQH LHSSRHRRAL DTNYCFSSTE KNCCVRQLYI
310 320 330 340 350
DFRKDLGWKW IHEPKGYHAN FCLGPCPYIW SLDTQYSKVL ALYNQHNPGA
360 370 380 390
SASPCCVPQA LEPLPIVYYV GRKPKVEQLS NMIVRSCKCS

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-6209 Collapse assay details

Data source: Panorama

Official Gene Symbol

TGFB1

Peptide Sequence

EAVPEPVLLSR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

7

Peptide Start

142

Peptide End

152

CPTAC ID

CPTAC-6209

Peptide Molecular Mass

1,208.6765

Species

Homo Sapiens

Assay Type

Enrichment MRM

Enrichment Method

IMAC

Matrix

Frozen tissue

Submitting Laboratory

Fred Hutchinson Cancer Research Center

Submitting Lab PI

Amanda Paulovich

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

QTRAP 5500

Internal Standard

Extended heavy peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Eksigent

Column Packing

Reprosil C18, 3um

Column Dimensions

75µm x 15cm

Flow Rate

0.3 µL/min

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

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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 | | y6 (1+) | 8.2 | 3.5 | 5 | 7.5 | 4.6 | 7.2 | 11.1 | 5.8 | 8.8 | 15 | 15 | 15 | | y8 (1+) | 6.1 | 4.3 | 5 | 11.5 | 4.4 | 7.9 | 13 | 6.2 | 9.3 | 15 | 15 | 15 | | y8 (2+) | 6.6 | 4 | 4.1 | 7.9 | 4 | 7.8 | 10.3 | 5.7 | 8.8 | 15 | 15 | 15 | | sum | 6.1 | 3.5 | 4.4 | 8.6 | 3.8 | 7.5 | 10.5 | 5.2 | 8.7 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-3952 Collapse assay details

Data source: Panorama

Official Gene Symbol

Tgfb1

Peptide Sequence

LHVEINGISPK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

232

Peptide End

242

CPTAC ID

non-CPTAC-3952

Peptide Molecular Mass

1,205.6768

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

>80%

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

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+) | 8.1 | 4.5 | 5.3 | 8.7 | 7.7 | 6.6 | 11.9 | 8.9 | 8.5 | 15 | 15 | 15 | | y3 (1+) | 5 | 4.8 | 2.9 | 8.8 | 5.9 | 4.3 | 10.1 | 7.6 | 5.2 | 15 | 15 | 15 | | b3 (1+) | 9.6 | 4.1 | 4.6 | 15.9 | 6.3 | 7.9 | 18.6 | 7.5 | 9.1 | 15 | 15 | 15 | | b4 (1+) | 7.4 | 4.7 | 3.4 | 11 | 6.7 | 5.6 | 13.3 | 8.2 | 6.6 | 15 | 15 | 15 | | b5 (1+) | 9.8 | 5.1 | 4.4 | 10.1 | 9.8 | 6.3 | 14.1 | 11 | 7.7 | 15 | 15 | 15 | | sum | 2.2 | 2.8 | 1.5 | 5.7 | 5.7 | 4.3 | 6.1 | 6.4 | 4.6 | 15 | 15 | 15 |

Additional Resources and Comments