ILF3, CPTAC-395 - 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-6103: View additional IFVNDDR data

10 20 30 40 50
MRPMRIFVND DRHVMAKHSS VYPTQEELEA VQNMVSHTER ALKAVSDWID
60 70 80 90 100
EQEKGSSEQA ESDNMDVPPE DDSKEGAGEQ KTEHMTRTLR GVMRVGLVAK
110 120 130 140 150
GLLLKGDLDL ELVLLCKEKP TTALLDKVAD NLAIQLAAVT EDKYEILQSV
160 170 180 190 200
DDAAIVIKNT KEPPLSLTIH LTSPVVREEM EKVLAGETLS VNDPPDVLDR
210 220 230 240 250
QKCLAALASL RHAKWFQARA NGLKSCVIVI RVLRDLCTRV PTWGPLRGWP
260 270 280 290 300
LELLCEKSIG TANRPMGAGE ALRRVLECLA SGIVMPDGSG IYDPCEKEAT
310 320 330 340 350
DAIGHLDRQQ REDITQSAQH ALRLAAFGQL HKVLGMDPLP SKMPKKPKNE
360 370 380 390 400
NPVDYTVQIP PSTTYAITPM KRPMEEDGEE KSPSKKKKKI QKKEEKAEPP
410 420 430 440 450
QAMNALMRLN QLKPGLQYKL VSQTGPVHAP IFTMSVEVDG NSFEASGPSK
460 470 480 490 500
KTAKLHVAVK VLQDMGLPTG AEGRDSSKGE DSAEETEAKP AVVAPAPVVE
510 520 530 540 550
AVSTPSAAFP SDATAEQGPI LTKHGKNPVM ELNEKRRGLK YELISETGGS
560 570 580 590 600
HDKRFVMEVE VDGQKFQGAG SNKKVAKAYA ALAALEKLFP DTPLALDANK
610 620 630 640 650
KKRAPVPVRG GPKFAAKPHN PGFGMGGPMH NEVPPPPNLR GRGRGGSIRG
660 670 680 690 700
RGRGRGFGGA NHGGYMNAGA GYGSYGYGGN SATAGYSQFY SNGGHSGNAS
710 720 730 740 750
GGGGGGGGGS SGYGSYYQGD NYNSPVPPKH AGKKQPHGGQ QKPSYGSGYQ
760 770 780 790 800
SHQGQQQSYN QSPYSNYGPP QGKQKGYNHG QGSYSYSNSY NSPGGGGGSD
810 820 830 840 850
YNYESKFNYS GSGGRSGGNS YGSGGASYNP GSHGGYGGGS GGGSSYQGKQ
860 870 880 890 894
GGYSQSNYNS PGSGQNYSGP PSSYQSSQGG YGRNADHSMN YQYR

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-395 Collapse assay details

Data source: Panorama

Official Gene Symbol

ILF3

Peptide Sequence

AVSDWIDEQEK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

44

Peptide End

54

CPTAC ID

CPTAC-395

Peptide Molecular Mass

1,318.6041

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+) | 7.4 | 8.3 | 4.7 | 17.1 | 24 | 12 | 18.6 | 25.4 | 12.9 | 25 | 15 | 15 | | y7 (1+) | 7.8 | 9.3 | 9.5 | 18.7 | 25.8 | 24.1 | 20.3 | 27.4 | 25.9 | 25 | 15 | 15 | | y6 (1+) | 9.9 | 10.3 | 7.6 | 18.7 | 20.5 | 13.4 | 21.2 | 22.9 | 15.4 | 25 | 15 | 15 | | sum | 6.4 | 8.1 | 5.8 | 16.8 | 22.1 | 13.6 | 18 | 23.5 | 14.8 | 25 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-396 Collapse assay details

Data source: Panorama

Official Gene Symbol

ILF3

Peptide Sequence

VLAGETLSVNDPPDVLDR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

183

Peptide End

200

CPTAC ID

CPTAC-396

Peptide Molecular Mass

1,908.9793

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 | | y11 (1+) | 23.7 | 6.5 | 4 | 28.5 | 14.4 | 16.9 | 37.1 | 15.8 | 17.4 | 15 | 25 | 15 | | y10 (1+) | 26 | 11.3 | 7.1 | 34.9 | 15.7 | 19.8 | 43.5 | 19.3 | 21 | 15 | 25 | 15 | | y9 (1+) | 26.8 | 10.3 | 7.5 | 37.4 | 15.2 | 19.5 | 46 | 18.4 | 20.9 | 15 | 25 | 15 | | sum | 15.7 | 6.9 | 4.2 | 27.5 | 13.8 | 17.6 | 31.7 | 15.4 | 18.1 | 15 | 25 | 15 |

Additional Resources and Comments

Assay Details for non-CPTAC-6103 Collapse assay details

Data source: Panorama

Official Gene Symbol

ILF3

Peptide Sequence

IFVNDDR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

6

Peptide End

12

CPTAC ID

non-CPTAC-6103

Peptide Molecular Mass

877.4294

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

Bovine Serum Albumin

Submitting Laboratory

McGill University

Submitting Lab PI

Christoph H. Borchers, Gerald Batist

Publication

View Details (opens in a new window)

mTORC1-driven protein translation correlates with clinical benefit of capivasertib within a genetically preselected cohort of PIK3CA-altered tumours. Constance A Sobsey, Bjoern C Froehlich, Georgia Mitsa, Sahar Ibrahim, Robert Popp, Rene P Zahedi, Elza C de Bruin, Christoph H Borchers, Gerald Batist

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Agilent 6495B QQQ-MS

Internal Standard

Standard Isotope labeled internal standard peptides with 13Cx, 15Ny (R+10 or K+8)

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Infinity 1290

Column Packing

commercial (Agilent ZORBAX Eclipse Plus C18)

Column Dimensions

4.6 mm × 150 mm, (5 µm)

Flow Rate

0.4 mL/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 | | y2 (1+) | 2.3 | 1.6 | 1.6 | 2.1 | 2 | 1.9 | 3.1 | 2.6 | 2.5 | 16 | 16 | 17 | | y4 (1+) | 3.2 | 1.7 | 1.9 | 3.8 | 1.6 | 2.1 | 5 | 2.3 | 2.8 | 16 | 16 | 17 | | y5 (1+) | 1.5 | 1.9 | 1.3 | 1.7 | 2.3 | 3.9 | 2.3 | 3 | 4.1 | 16 | 16 | 17 | | y6 (1+) | 1.7 | 1.4 | 2.1 | 2.3 | 1.1 | 1.9 | 2.9 | 1.8 | 2.8 | 16 | 16 | 17 | | y6 (2+) | 7 | 3.9 | 2.6 | 6.4 | 3.7 | 2.5 | 9.5 | 5.4 | 3.6 | 16 | 16 | 17 | | sum | 0.7 | 0.9 | 0.8 | 1.2 | 1.2 | 2.5 | 1.4 | 1.5 | 2.6 | 16 | 16 | 17 |

Additional Resources and Comments