Efemp1, CPTAC-3805 - 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.

Overview Data source: UniProt

Protein Sequence hover to view complete sequence

non-CPTAC-5606: View additional ELPQSIVYK data

non-CPTAC-3805: View additional SGNENGEFYLR data

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-5606 Collapse assay details

Data source: Panorama

Official Gene Symbol

Efemp1

Peptide Sequence

ELPQSIVYK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

388

Peptide End

396

CPTAC ID

non-CPTAC-5606

Peptide Molecular Mass

1,075.5914

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 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 | | b2 (1+) | 28.2 | 6.3 | 2.4 | 60.8 | 12.7 | 4.9 | 67 | 14.2 | 5.5 | 15 | 15 | 15 | | y7 (2+) | 2.8 | 1.6 | 1.5 | 5.7 | 6.4 | 3.6 | 6.4 | 6.6 | 3.9 | 15 | 15 | 15 | | y2 (1+) | 23.6 | 6.6 | 8.6 | 30.2 | 10.2 | 9.1 | 38.3 | 12.1 | 12.5 | 15 | 15 | 15 | | y5 (1+) | 11.1 | 3.2 | 4.5 | 12.7 | 6.8 | 5.1 | 16.9 | 7.5 | 6.8 | 15 | 15 | 15 | | y7 (1+) | 8.5 | 1.8 | 1.1 | 8.5 | 6.9 | 2.6 | 12 | 7.1 | 2.8 | 15 | 15 | 15 | | sum | 6.3 | 1.3 | 1.1 | 13.7 | 6.2 | 3.2 | 15.1 | 6.3 | 3.4 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-3805 Collapse assay details

Data source: Panorama

Official Gene Symbol

Efemp1

Peptide Sequence

SGNENGEFYLR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

430

Peptide End

440

CPTAC ID

non-CPTAC-3805

Peptide Molecular Mass

1,284.5735

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 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 | | y2 (1+) | 7.8 | 5.1 | 3.8 | 8.3 | 7.5 | 6.2 | 11.4 | 9.1 | 7.3 | 15 | 15 | 15 | | y3 (1+) | 18.1 | 4.7 | 6.2 | 17.7 | 8.9 | 7.8 | 25.3 | 10.1 | 10 | 15 | 15 | 15 | | y4 (1+) | 12.6 | 3.4 | 4.3 | 15.5 | 4.1 | 7 | 20 | 5.3 | 8.2 | 15 | 15 | 15 | | y6 (1+) | 10.4 | 7.4 | 4.6 | 13 | 9.3 | 5.5 | 16.6 | 11.9 | 7.2 | 15 | 15 | 15 | | y7 (1+) | 10.1 | 4.1 | 5.4 | 9.9 | 8.3 | 5.9 | 14.1 | 9.3 | 8 | 15 | 15 | 15 | | sum | 5.7 | 1.7 | 2.7 | 7 | 4.9 | 3.8 | 9 | 5.2 | 4.7 | 15 | 15 | 15 |

Additional Resources and Comments