PNP, CPTAC-570 - 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

CPTAC-571: View additional VFGFSLITNK data

10	20	30	40	50
MENGYTYEDY	KNTAEWLLSH	TKHRPQVAII	CGSGLGGLTD	KLTQAQIFDY
60	70	80	90	100
GEIPNFPRST	VPGHAGRLVF	GFLNGRACVM	MQGRFHMYEG	YPLWKVTFPV
110	120	130	140	150
RVFHLLGVDT	LVVTNAAGGL	NPKFEVGDIM	LIRDHINLPG	FSGQNPLRGP
160	170	180	190	200
NDERFGDRFP	AMSDAYDRTM	RQRALSTWKQ	MGEQRELQEG	TYVMVAGPSF
210	220	230	240	250
ETVAECRVLQ	KLGADAVGMS	TVPEVIVARH	CGLRVFGFSL	ITNKVIMDYE
260	270	280	289
SLEKANHEEV	LAAGKQAAQK	LEQFVSILMA	SIPLPDKAS

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-570 Collapse assay details

Data source: Panorama

Official Gene Symbol

PNP

Peptide Sequence

DHINLPGFSGQNPLR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

134

Peptide End

148

CPTAC ID

CPTAC-570

Peptide Molecular Mass

1,663.8431

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

cell line lysate pool

Submitting Laboratory

Seoul National University / Korea Institute of Science and Technology and FHCRC

Submitting Lab PI

Youngsoo Kim

Publication

View Details (opens in a new window)

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253

Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

5500 QTRAP (ABSCIEX)

Internal Standard

peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C,15N

nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)

Column Packing

ChromXP C18-CL, 3 um, 120A

Column Dimensions

150 x 0.075 mm

Flow Rate

500 nL / 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 CV equation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y11 (1+) | 26.7 | 24.8 | 21.7 | 46.5 | 29.9 | 35.6 | 53.6 | 38.8 | 41.7 | 15 | 25 | 15 | | y10 (1+) | 35 | 8.4 | 7.7 | 42 | 17.2 | 13.7 | 54.7 | 19.1 | 15.7 | 15 | 25 | 15 | | y9 (1+) | 46.9 | 39.8 | 24.6 | 47 | 44.1 | 30.6 | 66.4 | 59.4 | 39.3 | 15 | 25 | 15 | | sum | 26.9 | 8.3 | 7.3 | 33.5 | 16.5 | 15.3 | 43 | 18.5 | 17 | 15 | 25 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-571 Collapse assay details

Data source: Panorama

Official Gene Symbol

PNP

Peptide Sequence

VFGFSLITNK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

235

Peptide End

244

CPTAC ID

CPTAC-571

Peptide Molecular Mass

1,124.6230

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

cell line lysate pool

Submitting Laboratory

Seoul National University / Korea Institute of Science and Technology and FHCRC

Submitting Lab PI

Youngsoo Kim

Publication

View Details (opens in a new window)

Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

5500 QTRAP (ABSCIEX)

Internal Standard

peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C,15N

nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)

Column Packing

ChromXP C18-CL, 3 um, 120A

Column Dimensions

150 x 0.075 mm

Flow Rate

500 nL / 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 CV equation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y8 (1+) | 10.2 | 6.6 | 5 | 17.5 | 7.4 | 4.1 | 20.3 | 9.9 | 6.5 | 15 | 25 | 15 | | y7 (1+) | 20.1 | 8 | 6 | 32.6 | 10.4 | 7.2 | 38.3 | 13.1 | 9.4 | 15 | 25 | 15 | | y6 (1+) | 12.3 | 6.6 | 5.4 | 17.5 | 7.6 | 6.6 | 21.4 | 10.1 | 8.5 | 15 | 25 | 15 | | sum | 9.6 | 6.1 | 4.7 | 15.1 | 6.8 | 3.8 | 17.9 | 9.1 | 6 | 15 | 25 | 15 |