NPEPPS, CPTAC-415 - 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-416: View additional SPVYLTVLK data

10 20 30 40 50
MWLAAAAPSL ARRLLFLGPP PPPLLLLVFS RSSRRRLHSL GLAAMPEKRP
60 70 80 90 100
FERLPADVSP INYSLCLKPD LLDFTFEGKL EAAAQVRQAT NQIVMNCADI
110 120 130 140 150
DIITASYAPE GDEEIHATGF NYQNEDEKVT LSFPSTLQTG TGTLKIDFVG
160 170 180 190 200
ELNDKMKGFY RSKYTTPSGE VRYAAVTQFE ATDARRAFPC WDEPAIKATF
210 220 230 240 250
DISLVVPKDR VALSNMNVID RKPYPDDENL VEVKFARTPV MSTYLVAFVV
260 270 280 290 300
GEYDFVETRS KDGVCVRVYT PVGKAEQGKF ALEVAAKTLP FYKDYFNVPY
310 320 330 340 350
PLPKIDLIAI ADFAAGAMEN WGLVTYRETA LLIDPKNSCS SSRQWVALVV
360 370 380 390 400
GHELAHQWFG NLVTMEWWTH LWLNEGFASW IEYLCVDHCF PEYDIWTQFV
410 420 430 440 450
SADYTRAQEL DALDNSHPIE VSVGHPSEVD EIFDAISYSK GASVIRMLHD
460 470 480 490 500
YIGDKDFKKG MNMYLTKFQQ KNAATEDLWE SLENASGKPI AAVMNTWTKQ
510 520 530 540 550
MGFPLIYVEA EQVEDDRLLR LSQKKFCAGG SYVGEDCPQW MVPITISTSE
560 570 580 590 600
DPNQAKLKIL MDKPEMNVVL KNVKPDQWVK LNLGTVGFYR TQYSSAMLES
610 620 630 640 650
LLPGIRDLSL PPVDRLGLQN DLFSLARAGI ISTVEVLKVM EAFVNEPNYT
660 670 680 690 700
VWSDLSCNLG ILSTLLSHTD FYEEIQEFVK DVFSPIGERL GWDPKPGEGH
710 720 730 740 750
LDALLRGLVL GKLGKAGHKA TLEEARRRFK DHVEGKQILS ADLRSPVYLT
760 770 780 790 800
VLKHGDGTTL DIMLKLHKQA DMQEEKNRIE RVLGATLLPD LIQKVLTFAL
810 820 830 840 850
SEEVRPQDTV SVIGGVAGGS KHGRKAAWKF IKDNWEELYN RYQGGFLISR
860 870 880 890 900
LIKLSVEGFA VDKMAGEVKA FFESHPAPSA ERTIQQCCEN ILLNAAWLKR
910 919
DAESIHQYLL QRKASPPTV

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-415 Collapse assay details

Data source: Panorama

Official Gene Symbol

NPEPPS

Peptide Sequence

LGLQNDLFSLAR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

616

Peptide End

627

CPTAC ID

CPTAC-415

Peptide Molecular Mass

1,345.7354

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

cell line lysate pool

Submitting Laboratory

Broad Institute and FHCRC

Submitting Lab PI

Steve Carr

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 Broad Institute. Repeatability data acquired at Fred Hutchinson Cancer Research Center.

Response curves acquired at Broad Institute. 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

LC

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 CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y9 (1+) | 12 | 14 | 8.6 | 24.1 | 20.2 | 22 | 26.9 | 24.6 | 23.6 | 15 | 25 | 15 | | y8 (1+) | 8.2 | 6.9 | 3.9 | 23.2 | 11.9 | 7.7 | 24.6 | 13.8 | 8.6 | 15 | 25 | 15 | | y6 (1+) | 9.7 | 10.7 | 6.1 | 23 | 15.3 | 15.6 | 25 | 18.7 | 16.8 | 15 | 25 | 15 | | sum | 7 | 8.9 | 5.1 | 21.9 | 14.5 | 11.1 | 23 | 17 | 12.2 | 15 | 25 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-416 Collapse assay details

Data source: Panorama

Official Gene Symbol

NPEPPS

Peptide Sequence

SPVYLTVLK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

745

Peptide End

753

CPTAC ID

CPTAC-416

Peptide Molecular Mass

1,018.6063

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

cell line lysate pool

Submitting Laboratory

Broad Institute and FHCRC

Submitting Lab PI

Steve Carr

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 Broad Institute. Repeatability data acquired at Fred Hutchinson Cancer Research Center.

Response curves acquired at Broad Institute. 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

LC

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 CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y7 (1+) | 12.6 | 7.6 | 5.6 | 16.5 | 9.5 | 8.6 | 20.8 | 12.2 | 10.3 | 15 | 25 | 15 | | y6 (1+) | 14 | 5.2 | 3.5 | 17.2 | 5.6 | 4.3 | 22.2 | 7.6 | 5.5 | 15 | 25 | 15 | | y5 (1+) | 24.3 | 7.5 | 7.6 | 24.5 | 8.1 | 8.3 | 34.5 | 11 | 11.3 | 15 | 25 | 15 | | sum | 12.2 | 4.2 | 3.1 | 11.8 | 5.1 | 4.5 | 17 | 6.6 | 5.5 | 15 | 25 | 15 |

Additional Resources and Comments