APOB, CPTAC-652 - CPTAC Assay Portal (original) (raw)

Please include the following statement when referencing the CPTAC Assay Portal

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-1080: View additional FPEVDVLTK data

non-CPTAC-5577: View additional LSLEDTPK data

non-CPTAC-1081: View additional TGISPLALIK data

Data source: UniProt

Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Uniprot Database Entry PhosphoSitePlus ®

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to view detailed assay information below

All other points link out to UniProt

Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-2205 Collapse assay details

Data source: Panorama

Official Gene Symbol

APOB

Peptide Modified Sequence

FEVDSPVYN[+1.0]ATWSASLK

Modification Type

Deamidated (N)

Protein - Site of Modification

3895

Peptide - Site of Modification

9

Peptide Start

3887

Peptide End

3903

CPTAC ID

CPTAC-2205

Peptide Molecular Mass

1,913.9047

Species

Homo sapiens (Human)

Assay Type

Direct PRM

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 K

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

Johns Hopkins University-A

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 | | y7 (1+) | 32 | 7.6 | 9.1 | 33.9 | 12.2 | 12.5 | 46.6 | 14.4 | 15.5 | 15 | 15 | 15 | | y6 (1+) | 16.6 | 6.4 | 8.5 | 29.8 | 8.6 | 9.4 | 34.1 | 10.7 | 12.7 | 15 | 15 | 15 | | y5 (1+) | 33.2 | 8 | 10.2 | 24.9 | 12.3 | 10.1 | 41.5 | 14.7 | 14.4 | 15 | 15 | 15 | | sum | 22.4 | 3.8 | 4.9 | 24.9 | 3.8 | 5 | 33.5 | 5.4 | 7 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-652 Collapse assay details

Data source: Panorama

Official Gene Symbol

APOB

Peptide Modified Sequence

FN[+1.0]SSYLQGTNQITGR

Modification Type

Deamidated (NQ)

Protein - Site of Modification

1523

Peptide - Site of Modification

2

Peptide Start

1522

Peptide End

1536

CPTAC ID

CPTAC-652

Peptide Molecular Mass

1,685.8009

Species

Homo sapiens (Human)

Assay Type

Enrichment PRM

Enrichment Method

N-linked glycopeptide solid phase extraction

Matrix

serum

Submitting Laboratory

Johns Hopkins University

Submitting Lab PI

Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Q-Exactive (ThermoFisher)

Internal Standard

synthetic peptide

Peptide Standard Purity

Crude

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Dionex UltiMate 3000 RSLCnano LC (ThermoFisher)

Column Packing

Acclaim PepMap100 C18, 5um (Trap); Acclaim PepMap RSLC C18, 2um (Analytical)

Column Dimensions

300um x 5mm (Trap); 75um x 25cm (Analytical)

Flow Rate

0.5 uL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

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 | | y10 (1+) | 3.1 | 4.6 | 7.3 | 4.7 | 4.5 | 7.3 | 5.6 | 6.4 | 10.3 | 15 | 15 | 15 | | y9 (1+) | 4.5 | 3.7 | 5.7 | 5 | 3.5 | 5.9 | 6.7 | 5.1 | 8.2 | 15 | 15 | 15 | | y8 (1+) | 3.6 | 3.9 | 6.1 | 5.2 | 3.8 | 6.1 | 6.3 | 5.4 | 8.6 | 15 | 15 | 15 | | sum | 3.4 | 3.8 | 5.9 | 4.4 | 3.4 | 6.2 | 5.6 | 5.1 | 8.6 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-1299 Collapse assay details

Data source: Panorama

Official Gene Symbol

APOB

Peptide Modified Sequence

FN[+1.0]SSYLQGTNQITGR

Modification Type

Deamidated (N)

Protein - Site of Modification

1523

Peptide - Site of Modification

2

Peptide Start

1522

Peptide End

1536

CPTAC ID

CPTAC-1299

Peptide Molecular Mass

1,685.8009

Species

Homo sapiens (Human)

Assay Type

Direct PRM

Matrix

Human ovarian tumor 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

TSQ Vantage

Internal Standard

Stable isotope-labeled peptides

Peptide Standard Purity

Crude (~60%)

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Accela 1250 Quaternary Low Pump

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

Johns Hopkins University-A

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 (1+) | 16.3 | 9.2 | 6.3 | 19.2 | 9.8 | 8.1 | 25.2 | 13.4 | 10.3 | 15 | 15 | 15 | | y9 (1+) | 15.9 | 7 | 7.5 | 25.1 | 7.4 | 7.9 | 29.7 | 10.2 | 10.9 | 15 | 15 | 15 | | y10 (1+) | 16.9 | 16.2 | 5.5 | 19.3 | 16.1 | 10 | 25.7 | 22.8 | 11.4 | 15 | 15 | 15 | | sum | 9.2 | 6.3 | 4.2 | 15.6 | 6 | 5.3 | 18.1 | 8.7 | 6.8 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-1300 Collapse assay details

Data source: Panorama

Official Gene Symbol

APOB

Peptide Modified Sequence

FVEGSHN[+1.0]STVSLTTK

Modification Type

Deamidated (N)

Protein - Site of Modification

3411

Peptide - Site of Modification

7

Peptide Start

3405

Peptide End

3419

CPTAC ID

CPTAC-1300

Peptide Molecular Mass

1,606.7839

Species

Homo sapiens (Human)

Assay Type

Direct PRM

Matrix

Human ovarian tumor 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

TSQ Vantage

Internal Standard

Stable isotope-labeled peptides

Peptide Standard Purity

Crude (~60%)

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

Accela 1250 Quaternary Low Pump

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

Johns Hopkins University-A

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 | | y13 (2+) | 30.7 | 21.5 | 20.6 | 37 | 21.5 | 21 | 48.1 | 30.4 | 29.4 | 15 | 15 | 15 | | y5 (1+) | 56 | 18 | 31.2 | 49.1 | 29.2 | 30.6 | 74.5 | 34.3 | 43.7 | 15 | 15 | 15 | | y12 (2+) | 40.8 | 42.8 | 32.6 | 45.5 | 48 | 30.9 | 61.1 | 64.3 | 44.9 | 15 | 15 | 15 | | sum | 26.3 | 12.2 | 16.6 | 29.1 | 16.8 | 17.5 | 39.2 | 20.8 | 24.1 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-653 Collapse assay details

Data source: Panorama

Official Gene Symbol

APOB

Peptide Modified Sequence

YDFN[+1.0]SSM[+16.0]LYSTAK

Modification Type

Deamidated (NQ), Oxidation (M)

Protein - Site of Modification

3465, 3468

Peptide - Site of Modification

4, 7

Peptide Start

3462

Peptide End

3474

CPTAC ID

CPTAC-653

Peptide Molecular Mass

1,542.6548

Species

Homo sapiens (Human)

Assay Type

Enrichment PRM

Enrichment Method

N-linked glycopeptide solid phase extraction

Matrix

serum

Submitting Laboratory

Johns Hopkins University

Submitting Lab PI

Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Q-Exactive (ThermoFisher)

Internal Standard

synthetic peptide

Peptide Standard Purity

Crude

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

Dionex UltiMate 3000 RSLCnano LC (ThermoFisher)

Column Packing

Acclaim PepMap100 C18, 5um (Trap); Acclaim PepMap RSLC C18, 2um (Analytical)

Column Dimensions

300um x 5mm (Trap); 75um x 25cm (Analytical)

Flow Rate

0.5 uL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

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 | | y10 (1+) | 4.8 | 4.8 | 5.7 | 4.9 | 5.3 | 6.2 | 6.9 | 7.2 | 8.4 | 15 | 15 | 15 | | y9 (1+) | 3.2 | 4.2 | 4.9 | 4.7 | 4.6 | 4.7 | 5.7 | 6.2 | 6.8 | 15 | 15 | 15 | | y8 (1+) | 4.6 | 5.4 | 6.4 | 3.9 | 4.9 | 5.5 | 6 | 7.3 | 8.4 | 15 | 15 | 15 | | sum | 3.6 | 4.4 | 4.9 | 4.2 | 4.6 | 5.3 | 5.5 | 6.4 | 7.2 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-1082 Collapse assay details

Data source: Panorama

Official Gene Symbol

APOB

Peptide Sequence

ATLYALSHAVNNYHK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

440

Peptide End

454

CPTAC ID

non-CPTAC-1082

Peptide Molecular Mass

1,700.8635

Species

Homo sapiens (Human)

Assay Type

Direct PRM

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

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

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 | | y12 (3+) | 5.5 | 4 | 4.5 | 6.9 | 6 | 6.5 | 8.8 | 7.2 | 7.9 | 15 | 15 | 15 | | y13 (3+) | 6.7 | 7.2 | 4.4 | 5.4 | 6.3 | 4.2 | 8.6 | 9.6 | 6.1 | 15 | 15 | 15 | | y10 (2+) | 8.4 | 6.2 | 5.7 | 9.5 | 6.4 | 5.4 | 12.7 | 8.9 | 7.9 | 15 | 15 | 15 | | y11 (2+) | 5.8 | 6 | 5.6 | 8.1 | 5.9 | 4.8 | 10 | 8.4 | 7.4 | 15 | 15 | 15 | | y12 (2+) | 6 | 6.2 | 3.6 | 7.8 | 8.8 | 5.1 | 9.8 | 10.8 | 6.2 | 15 | 15 | 15 | | sum | 4.2 | 3.7 | 3.4 | 4.9 | 4.1 | 2.9 | 6.5 | 5.5 | 4.5 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-1080 Collapse assay details

Data source: Panorama

Official Gene Symbol

APOB

Peptide Sequence

FPEVDVLTK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

3791

Peptide End

3799

CPTAC ID

non-CPTAC-1080

Peptide Molecular Mass

1,046.5648

Species

Homo sapiens (Human)

Assay Type

Direct PRM

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

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

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+) | 15.9 | 4.8 | 3 | 8.9 | 6.3 | 3.2 | 18.2 | 7.9 | 4.4 | 9 | 15 | 15 | | y8 (2+) | 5.1 | 4.2 | 3.2 | 8.2 | 4.4 | 4 | 9.7 | 6.1 | 5.1 | 15 | 15 | 15 | | y2 (1+) | 13.9 | 3.8 | 3.6 | 13.9 | 6.2 | 3.3 | 19.7 | 7.3 | 4.9 | 15 | 15 | 15 | | y7 (1+) | 4.5 | 3.6 | 3.4 | 9.5 | 6.5 | 3.7 | 10.5 | 7.4 | 5 | 15 | 15 | 15 | | y8 (1+) | 10.2 | 4.4 | 3.8 | 12.6 | 5.3 | 5 | 16.2 | 6.9 | 6.3 | 15 | 15 | 15 | | sum | 6.8 | 3.2 | 2.5 | 9.4 | 4.1 | 3.3 | 11.6 | 5.2 | 4.1 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-5577 Collapse assay details

Data source: Panorama

Official Gene Symbol

Apob

Peptide Sequence

LSLEDTPK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

286

Peptide End

293

CPTAC ID

non-CPTAC-5577

Peptide Molecular Mass

901.4757

Species

Mus musculus (Mouse)

Assay Type

Direct PRM

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

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

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+) | 8.4 | 4.5 | 4.7 | 9.6 | 7.9 | 4.1 | 12.8 | 9.1 | 6.2 | 15 | 15 | 15 | | y2 (1+) | 6.2 | 3 | 6.2 | 7.6 | 4.7 | 5.9 | 9.8 | 5.6 | 8.6 | 15 | 15 | 15 | | y5 (1+) | 8.2 | 3.4 | 4.5 | 8.8 | 7.2 | 5.6 | 12 | 8 | 7.2 | 15 | 15 | 15 | | y6 (1+) | 4.1 | 5.4 | 4.7 | 7 | 6.8 | 5 | 8.1 | 8.7 | 6.9 | 15 | 15 | 15 | | y7 (1+) | 6.9 | 5 | 5.4 | 7.1 | 6.5 | 4.5 | 9.9 | 8.2 | 7 | 15 | 15 | 15 | | sum | 2.6 | 1.9 | 1.9 | 5.1 | 5.6 | 3.1 | 5.7 | 5.9 | 3.6 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-1081 Collapse assay details

Data source: Panorama

Official Gene Symbol

APOB

Peptide Sequence

TGISPLALIK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

220

Peptide End

229

CPTAC ID

non-CPTAC-1081

Peptide Molecular Mass

1,011.6328

Species

Homo sapiens (Human)

Assay Type

Direct PRM

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

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

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+) | 8.7 | 2.4 | 4.8 | 8.5 | 3.2 | 5.1 | 12.2 | 4 | 7 | 15 | 15 | 15 | | y6 (1+) | 5.8 | 7.7 | 5.2 | 11.8 | 6.9 | 5.6 | 13.1 | 10.3 | 7.6 | 15 | 15 | 15 | | y7 (1+) | 6.2 | 5.1 | 4 | 9.4 | 5.8 | 6.5 | 11.3 | 7.7 | 7.6 | 15 | 15 | 15 | | sum | 4.2 | 3.2 | 2.8 | 8.2 | 4.4 | 4.2 | 9.2 | 5.4 | 5 | 15 | 15 | 15 |

Additional Resources and Comments