LRP1, CPTAC-1617 - 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

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-2223 Collapse assay details

Data source: Panorama

Official Gene Symbol

LRP1

Peptide Modified Sequence

DGTC[+57.0]IGN[+1.0]SSR

Modification Type

Carbamidomethyl (C), Deamidated (N)

Protein - Site of Modification

2617, 2620

Peptide - Site of Modification

4, 7

Peptide Start

2614

Peptide End

2623

CPTAC ID

CPTAC-2223

Peptide Molecular Mass

1,066.4349

Species

Homo sapiens (Human)

Assay Type

Direct MRM or SRM

Matrix

Human ovarian tissue digest

Submitting Laboratory

Johns Hopkins University

Submitting Lab PI

Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

LCMS-8040

Internal Standard

Stable isotope-labeled peptides

Peptide Standard Purity

Crude (~60%)

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Nexera X2 UHPLC

Column Packing

C18, 3 µm, 300 Å

Column Dimensions

1.0 mm I.D. x 15 cm

Flow Rate

50 µL/min

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectSRM3

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+) | 19.4 | 13.1 | 6.2 | 20.7 | 13.7 | 5.9 | 28.4 | 19 | 8.6 | 15 | 15 | 15 | | y5 (1+) | 8.8 | 5.1 | 3.9 | 9.9 | 4.7 | 3.5 | 13.2 | 6.9 | 5.2 | 15 | 15 | 15 | | y6 (1+) | 19.2 | 8 | 4.7 | 19 | 10.6 | 5.6 | 27 | 13.3 | 7.3 | 15 | 15 | 15 | | sum | 9.5 | 3.3 | 2.4 | 9.5 | 3.8 | 2.3 | 13.4 | 5 | 3.3 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-2222 Collapse assay details

Data source: Panorama

Official Gene Symbol

LRP1

Peptide Modified Sequence

ELQGN[+1.0]C[+57.0]SR

Modification Type

Deamidated (N), Carbamidomethyl (C)

Protein - Site of Modification

114, 115

Peptide - Site of Modification

5, 6

Peptide Start

110

Peptide End

117

CPTAC ID

CPTAC-2222

Peptide Molecular Mass

963.4080

Species

Homo sapiens (Human)

Assay Type

Direct MRM or SRM

Matrix

Human ovarian tissue digest

Submitting Laboratory

Johns Hopkins University

Submitting Lab PI

Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

LCMS-8040

Internal Standard

Stable isotope-labeled peptides

Peptide Standard Purity

Crude (~60%)

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Nexera X2 UHPLC

Column Packing

C18, 3 µm, 300 Å

Column Dimensions

1.0 mm I.D. x 15 cm

Flow Rate

50 µL/min

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectSRM3

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+) | 38.6 | 21.4 | 18.3 | 39 | 20.2 | 21.1 | 54.9 | 29.4 | 27.9 | 15 | 15 | 15 | | y5 (1+) | 22.7 | 10.6 | 10.6 | 16.8 | 15 | 8.2 | 28.2 | 18.4 | 13.4 | 15 | 15 | 15 | | y6 (1+) | 24.7 | 22.1 | 35.4 | 31.4 | 19.7 | 37.6 | 40 | 29.6 | 51.6 | 15 | 15 | 15 | | sum | 12.8 | 11 | 8.5 | 12.9 | 12.7 | 8.7 | 18.2 | 16.8 | 12.2 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-1617 Collapse assay details

Data source: Panorama

Official Gene Symbol

LRP1

Peptide Sequence

AALSGANVLTLIEK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

2361

Peptide End

2374

CPTAC ID

CPTAC-1617

Peptide Molecular Mass

1,398.8082

Species

Homo sapiens (Human)

Assay Type

Direct MRM or SRM

Matrix

Ovarian cancer tumor tissue lysate

Submitting Laboratory

Pacific Northwest National Laboratory

Submitting Lab PI

Tao Liu

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

TSQ Vantage

Internal Standard

peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

Waters nanoACQUITY (Part Number 176016000)

Column Packing

Waters BEH C18, 1.7 um 130 Å (Part Number 186007485)

Column Dimensions

100 um x 100 mm

Flow Rate

0.5 uL/min

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectSRM3

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+) | 26.1 | 9 | 8.9 | 32.6 | 13.5 | 10.8 | 41.8 | 16.2 | 14 | 15 | 15 | 15 | | y6 (1+) | 10.4 | 3.9 | 2.7 | 20 | 5.6 | 8.1 | 22.5 | 6.8 | 8.5 | 15 | 15 | 15 | | y8 (1+) | 12.7 | 3.9 | 2.7 | 21.8 | 4.8 | 8.4 | 25.2 | 6.2 | 8.8 | 15 | 15 | 15 | | sum | 7.4 | 2.9 | 1.5 | 15.2 | 4.9 | 7.8 | 16.9 | 5.7 | 7.9 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-3838 Collapse assay details

Data source: Panorama

Official Gene Symbol

Lrp1

Peptide Sequence

TNTQPFDLQVYHPSR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

1519

Peptide End

1533

CPTAC ID

non-CPTAC-3838

Peptide Molecular Mass

1,801.8747

Species

Mus musculus (Mouse)

Assay Type

Direct MRM or SRM

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

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectSRM3

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 | | y11 (2+) | 14.8 | 2.9 | 4.1 | 12.6 | 6.1 | 6.6 | 19.4 | 6.8 | 7.8 | 15 | 15 | 15 | | b2 (1+) | 25.4 | 10.1 | 6.1 | 209.4 | 100.3 | 8.3 | 210.9 | 100.8 | 10.3 | 15 | 15 | 15 | | b3 (1+) | 35.9 | 5.5 | 8.5 | 34.2 | 8.5 | 9.7 | 49.6 | 10.1 | 12.9 | 15 | 15 | 15 | | y3 (1+) | 15.6 | 4.2 | 4.1 | 58.1 | 11.7 | 6.2 | 60.2 | 12.4 | 7.4 | 15 | 15 | 15 | | y13 (2+) | 19 | 8.8 | 5.5 | 184.1 | 52 | 7.1 | 185.1 | 52.7 | 9 | 15 | 15 | 15 | | sum | 11.1 | 3.3 | 2.6 | 164 | 26.4 | 5.8 | 164.4 | 26.6 | 6.4 | 15 | 15 | 15 |

Additional Resources and Comments