PRTN3, CPTAC-1142 - 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-3494: View additional LGTQAPTPR data

non-CPTAC-1142: View additional LVNVVLGAHNVR data

10 20 30 40 50
MAHRPPSPAL ASVLLALLLS GAARAAEIVG GHEAQPHSRP YMASLQMRGN
60 70 80 90 100
PGSHFCGGTL IHPSFVLTAA HCLRDIPQRL VNVVLGAHNV RTQEPTQQHF
110 120 130 140 150
SVAQVFLNNY DAENKLNDVL LIQLSSPANL SASVATVQLP QQDQPVPHGT
160 170 180 190 200
QCLAMGWGRV GAHDPPAQVL QELNVTVVTF FCRPHNICTF VPRRKAGICF
210 220 230 240 250
GDSGGPLICD GIIQGIDSFV IWGCATRLFP DFFTRVALYV DWIRSTLRRV
256
EAKGRP

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-3494 Collapse assay details

Data source: Panorama

Official Gene Symbol

Prtn3

Peptide Sequence

LGTQAPTPR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

162

Peptide End

170

CPTAC ID

non-CPTAC-3494

Peptide Molecular Mass

939.5138

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

>95%

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

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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 | | y7 (2+) | 20.1 | 7.8 | 8.6 | 19.1 | 11.3 | 10.4 | 27.7 | 13.7 | 13.5 | 15 | 15 | 15 | | y2 (1+) | 38.2 | 10.9 | 6.4 | 37.9 | 13 | 6.4 | 53.8 | 17 | 9.1 | 15 | 15 | 15 | | y5 (1+) | 9.4 | 4.6 | 6.3 | 11.5 | 5.7 | 5.1 | 14.9 | 7.3 | 8.1 | 15 | 15 | 15 | | y6 (1+) | 22.2 | 2.8 | 8.2 | 25.5 | 9 | 8 | 33.8 | 9.4 | 11.5 | 15 | 15 | 15 | | y8 (1+) | 20.7 | 5 | 7.2 | 21.5 | 9.2 | 10.5 | 29.8 | 10.5 | 12.7 | 15 | 15 | 15 | | sum | 6.3 | 3.1 | 3.9 | 7.7 | 5.1 | 3.6 | 9.9 | 6 | 5.3 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-1142 Collapse assay details

Data source: Panorama

Official Gene Symbol

PRTN3

Peptide Sequence

LVNVVLGAHNVR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

80

Peptide End

91

CPTAC ID

non-CPTAC-1142

Peptide Molecular Mass

1,289.7568

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 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

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 (2+) | 6 | 6.8 | 5.1 | 5.8 | 12.2 | 6.8 | 8.3 | 14 | 8.5 | 15 | 15 | 15 | | y10 (2+) | 7.1 | 4.7 | 6.5 | 6 | 9.2 | 7.1 | 9.3 | 10.3 | 9.6 | 15 | 15 | 15 | | y11 (2+) | 4 | 4.8 | 5.6 | 7 | 10.1 | 8 | 8.1 | 11.2 | 9.8 | 15 | 15 | 15 | | y6 (1+) | 6.4 | 7 | 4.1 | 8.4 | 9 | 4.8 | 10.6 | 11.4 | 6.3 | 15 | 15 | 15 | | y7 (1+) | 7.6 | 6.1 | 4.9 | 8.4 | 9.1 | 4.7 | 11.3 | 11 | 6.8 | 15 | 15 | 15 | | sum | 5 | 4.5 | 4.6 | 4.8 | 9.2 | 5.6 | 6.9 | 10.2 | 7.2 | 15 | 15 | 15 |

Additional Resources and Comments