TIMP1, CPTAC-680 - 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.

TIMP1

Protein Sequence hover to view complete sequence

non-CPTAC-3503: View additional AVGNAADIR data

10 20 30 40 50
MAPFEPLASG ILLLLWLIAP SRACTCVPPH PQTAFCNSDL VIRAKFVGTP
60 70 80 90 100
EVNQTTLYQR YEIKMTKMYK GFQALGDAAD IRFVYTPAME SVCGYFHRSH
110 120 130 140 150
NRSEEFLIAG KLQDGLLHIT TCSFVAPWNS LSLAQRRGFT KTYTVGCEEC
160 170 180 190 200
TVFPCLSIPC KLQSGTHCLW TDQLLQGSEK GFQSRHLACL PREPGLCTWQ
207
SLRSQIA

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-680 Collapse assay details

Data source: Panorama

Official Gene Symbol

TIMP1

Peptide Modified Sequence

FVGTPEVN[+1.0]QTTLYQR

Modification Type

Deamidated (NQ)

Protein - Site of Modification

53

Peptide - Site of Modification

8

Peptide Start

46

Peptide End

60

CPTAC ID

CPTAC-680

Peptide Molecular Mass

1,752.8683

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

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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 | | y11 (1+) | 7.7 | 6.6 | 9.1 | 8.2 | 9.5 | 9.6 | 11.2 | 11.6 | 13.2 | 15 | 15 | 15 | | y9 (1+) | 13.1 | 12.8 | 8.4 | 14 | 11.6 | 11.6 | 19.2 | 17.3 | 14.3 | 15 | 15 | 15 | | y8 (1+) | 7.9 | 13.1 | 9.5 | 7.7 | 12.5 | 10.3 | 11 | 18.1 | 14 | 15 | 15 | 15 | | sum | 6.1 | 6.8 | 7.1 | 6.8 | 7.7 | 7.3 | 9.1 | 10.3 | 10.2 | 15 | 15 | 15 |

Additional Resources and Comments

Comments

Assay Details for non-CPTAC-3503 Collapse assay details

Data source: Panorama

Official Gene Symbol

Timp1

Peptide Sequence

AVGNAADIR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

75

Peptide End

83

CPTAC ID

non-CPTAC-3503

Peptide Molecular Mass

885.4668

Species

Mus musculus (Mouse)

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

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

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

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 | | y2 (1+) | 10.9 | 9.1 | 4.3 | 12.8 | 8.2 | 6.9 | 16.8 | 12.2 | 8.1 | 15 | 15 | 15 | | y3 (1+) | 20.5 | 9.3 | 8.7 | 22.5 | 12.9 | 10.9 | 30.4 | 15.9 | 13.9 | 15 | 15 | 15 | | y4 (1+) | 8.8 | 6.7 | 6.6 | 11.8 | 9 | 7.2 | 14.7 | 11.2 | 9.8 | 15 | 15 | 15 | | y5 (1+) | 12.9 | 9.6 | 8.6 | 11.7 | 8.6 | 9.7 | 17.4 | 12.9 | 13 | 15 | 15 | 15 | | y7 (1+) | 6.1 | 6.5 | 5.5 | 7.7 | 8.4 | 5 | 9.8 | 10.6 | 7.4 | 15 | 15 | 15 | | sum | 4.6 | 4.6 | 3.7 | 5.7 | 6.5 | 3.4 | 7.3 | 8 | 5 | 15 | 15 | 15 |

Additional Resources and Comments

Comments