LBP, CPTAC-1140 - 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-3836: View additional HIQLHDLDFQIR data

non-CPTAC-1140: View additional ITLPDFTGDLR data

10 20 30 40 50
MGALARALPS ILLALLLTST PEALGANPGL VARITDKGLQ YAAQEGLLAL
60 70 80 90 100
QSELLRITLP DFTGDLRIPH VGRGRYEFHS LNIHSCELLH SALRPVPGQG
110 120 130 140 150
LSLSISDSSI RVQGRWKVRK SFFKLQGSFD VSVKGISISV NLLLGSESSG
160 170 180 190 200
RPTVTASSCS SDIADVEVDM SGDLGWLLNL FHNQIESKFQ KVLESRICEM
210 220 230 240 250
IQKSVSSDLQ PYLQTLPVTT EIDSFADIDY SLVEAPRATA QMLEVMFKGE
260 270 280 290 300
IFHRNHRSPV TLLAAVMSLP EEHNKMVYFA ISDYVFNTAS LVYHEEGYLN
310 320 330 340 350
FSITDDMIPP DSNIRLTTKS FRPFVPRLAR LYPNMNLELQ GSVPSAPLLN
360 370 380 390 400
FSPGNLSVDP YMEIDAFVLL PSSSKEPVFR LSVATNVSAT LTFNTSKITG
410 420 430 440 450
FLKPGKVKVE LKESKVGLFN AELLEALLNY YILNTFYPKF NDKLAEGFPL
460 470 480 481
PLLKRVQLYD LGLQIHKDFL FLGANVQYMR V

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-3836 Collapse assay details

Data source: Panorama

Official Gene Symbol

Lbp

Peptide Sequence

HIQLHDLDFQIR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

455

Peptide End

466

CPTAC ID

non-CPTAC-3836

Peptide Molecular Mass

1,533.8052

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

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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 | | b6 (2+) | 8.8 | 7.2 | 10.8 | 11.1 | 6.8 | 15.8 | 14.2 | 9.9 | 19.1 | 15 | 15 | 15 | | b2 (1+) | 11.9 | 5.5 | 21.9 | 21.2 | 23.8 | 71.5 | 24.3 | 24.4 | 74.8 | 15 | 15 | 15 | | y4 (1+) | 16.5 | 12.8 | 15.5 | 17.3 | 10.4 | 15.9 | 23.9 | 16.5 | 22.2 | 15 | 15 | 15 | | y5 (1+) | 15.8 | 8 | 13.3 | 9.9 | 8.7 | 11.1 | 18.6 | 11.8 | 17.3 | 15 | 15 | 15 | | y7 (1+) | 8.1 | 6.5 | 7.2 | 9.3 | 6.8 | 11.6 | 12.3 | 9.4 | 13.7 | 15 | 15 | 15 | | sum | 4.7 | 3.7 | 5.7 | 5.2 | 4.4 | 18.9 | 7 | 5.7 | 19.7 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-1140 Collapse assay details

Data source: Panorama

Official Gene Symbol

LBP

Peptide Sequence

ITLPDFTGDLR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

57

Peptide End

67

CPTAC ID

non-CPTAC-1140

Peptide Molecular Mass

1,246.6558

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 | | b2 (1+) | 11 | 6.1 | 3.7 | 11.8 | 6 | 7.2 | 16.1 | 8.6 | 8.1 | 15 | 15 | 15 | | y9 (2+) | 7.6 | 7.9 | 5.4 | 8.9 | 9.8 | 7.3 | 11.7 | 12.6 | 9.1 | 15 | 15 | 15 | | y2 (1+) | 11 | 6.7 | 5.2 | 12.6 | 9.5 | 6.3 | 16.7 | 11.6 | 8.2 | 15 | 15 | 14 | | y6 (1+) | 11.7 | 5.2 | 6.6 | 10.5 | 10.4 | 9.6 | 15.7 | 11.6 | 11.6 | 15 | 15 | 14 | | y8 (1+) | 8.8 | 8 | 4.7 | 12 | 10.3 | 9 | 14.9 | 13 | 10.2 | 15 | 15 | 14 | | sum | 7.3 | 4.6 | 5.8 | 9.3 | 7.5 | 6.1 | 11.8 | 8.8 | 8.4 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-3555 Collapse assay details

Data source: Panorama

Official Gene Symbol

Lbp

Peptide Sequence

LLPGQGLSLAISDSSIGVR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

95

Peptide End

113

CPTAC ID

non-CPTAC-3555

Peptide Molecular Mass

1,882.0524

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

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 | | b2 (1+) | 5.6 | 4 | 6 | 15.6 | 4.1 | 9.9 | 16.6 | 5.7 | 11.6 | 15 | 15 | 15 | | y17 (3+) | 6.3 | 2.9 | 6.1 | 15.4 | 3.4 | 9.2 | 16.6 | 4.5 | 11 | 15 | 15 | 15 | | y17 (2+) | 5.2 | 5.6 | 5.5 | 17.7 | 9.3 | 7.6 | 18.4 | 10.9 | 9.4 | 15 | 15 | 15 | | y6 (1+) | 7.8 | 6.4 | 6 | 14.6 | 8.1 | 9.5 | 16.6 | 10.3 | 11.2 | 15 | 15 | 15 | | y8 (1+) | 9 | 5.5 | 4 | 14.1 | 3.8 | 5.5 | 16.7 | 6.7 | 6.8 | 15 | 15 | 15 | | sum | 3.6 | 1.8 | 3.4 | 14.7 | 3.1 | 5.8 | 15.1 | 3.6 | 6.7 | 15 | 15 | 15 |

Additional Resources and Comments