CLIC1, CPTAC-1393 - 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-1397: View additional GFTIPEAFR data

CPTAC-1394: View additional YLSNAYAR data

non-CPTAC-3969: View additional NSNPALNDNLEK data

10 20 30 40 50
MAEEQPQVEL FVKAGSDGAK IGNCPFSQRL FMVLWLKGVT FNVTTVDTKR
60 70 80 90 100
RTETVQKLCP GGQLPFLLYG TEVHTDTNKI EEFLEAVLCP PRYPKLAALN
110 120 130 140 150
PESNTAGLDI FAKFSAYIKN SNPALNDNLE KGLLKALKVL DNYLTSPLPE
160 170 180 190 200
EVDETSAEDE GVSQRKFLDG NELTLADCNL LPKLHIVQVV CKKYRGFTIP
210 220 230 240 241
EAFRGVHRYL SNAYAREEFA STCPDDEEIE LAYEQVAKAL K

Data source: UniProt


Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Uniprot Database Entry PhosphoSitePlus ®

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All other points link out to UniProt


Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-1397 Collapse assay details

Data source: Panorama

Official Gene Symbol

CLIC1

Peptide Sequence

GFTIPEAFR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

196

Peptide End

204

CPTAC ID

CPTAC-1397

Peptide Molecular Mass

1,036.5342

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

depleted digested plasma

Submitting Laboratory

Broad Institute

Submitting Lab PI

Steven A. Carr


Publication

View Details (opens in a new window)

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18. PMID: 25693799


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Quantiva TSQ

Internal Standard

heavy stable isotope peptide (delta 8-10)

Peptide Standard Purity

>95%

Peptide Standard Label Type

15N

LC

Easy NanoLC1000

Column Packing

Reprosil C18, 1.9um, 200A

Column Dimensions

0.075 x 150 mm

Flow Rate

200 nL/min


Assay Multiplexing Expand assay panel

Broad Institute-Plasma-based Candidate Cancer Biomarkers


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+) | 5.6 | 2.8 | 2 | 10.3 | 5.2 | 4.3 | 11.7 | 5.9 | 4.7 | 15 | 15 | 15 | | y6 (1+) | 3.3 | 1.8 | 2.3 | 9.5 | 6.3 | 3.9 | 10.1 | 6.6 | 4.5 | 15 | 15 | 15 | | y5 (1+) | 1.6 | 1.7 | 1.1 | 9 | 7 | 3.4 | 9.1 | 7.2 | 3.6 | 15 | 15 | 15 | | sum | 1.5 | 1.6 | 0.9 | 9 | 6.8 | 3.4 | 9.1 | 7 | 3.5 | 15 | 15 | 15 |



Additional Resources and Comments


Assay Details for CPTAC-1396 Collapse assay details

Data source: Panorama

Official Gene Symbol

CLIC1

Peptide Sequence

GVTFNVTTVDTK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

38

Peptide End

49

CPTAC ID

CPTAC-1396

Peptide Molecular Mass

1,280.6612

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

depleted digested plasma

Submitting Laboratory

Broad Institute

Submitting Lab PI

Steven A. Carr


Publication

View Details (opens in a new window)

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18. PMID: 25693799


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Quantiva TSQ

Internal Standard

heavy stable isotope peptide (delta 8-10)

Peptide Standard Purity

>95%

Peptide Standard Label Type

15N

LC

Easy NanoLC1000

Column Packing

Reprosil C18, 1.9um, 200A

Column Dimensions

0.075 x 150 mm

Flow Rate

200 nL/min


Assay Multiplexing Expand assay panel

Broad Institute-Plasma-based Candidate Cancer Biomarkers


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 | | y8 (1+) | 7 | 1.7 | 1.2 | 5.8 | 6.5 | 3.8 | 9.1 | 6.7 | 4 | 15 | 15 | 15 | | y7 (1+) | 7.2 | 2.1 | 1.5 | 12.5 | 5.3 | 4.3 | 14.4 | 5.7 | 4.6 | 15 | 15 | 15 | | y6 (1+) | 5.1 | 1.8 | 1.8 | 6.3 | 6.4 | 3.1 | 8.1 | 6.6 | 3.6 | 15 | 15 | 15 | | sum | 2.7 | 0.8 | 1 | 6 | 6 | 3.3 | 6.6 | 6.1 | 3.4 | 15 | 15 | 15 |



Additional Resources and Comments


Assay Details for CPTAC-1395 Collapse assay details

Data source: Panorama

Official Gene Symbol

CLIC1

Peptide Modified Sequence

IEEFLEAVLC[+57.0]PPR

Modification Type

Carbamidomethyl Cysteine

Protein - Site of Modification

89

Peptide - Site of Modification

10

Peptide Start

80

Peptide End

92

CPTAC ID

CPTAC-1395

Peptide Molecular Mass

1,571.8018

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

depleted digested plasma

Submitting Laboratory

Broad Institute

Submitting Lab PI

Steven A. Carr


Publication

View Details (opens in a new window)

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18. PMID: 25693799


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Quantiva TSQ

Internal Standard

heavy stable isotope peptide (delta 8-10)

Peptide Standard Purity

>95%

Peptide Standard Label Type

15N

LC

Easy NanoLC1000

Column Packing

Reprosil C18, 1.9um, 200A

Column Dimensions

0.075 x 150 mm

Flow Rate

200 nL/min


Assay Multiplexing Expand assay panel

Broad Institute-Plasma-based Candidate Cancer Biomarkers


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 | | y6 (1+) | 26.2 | 7.4 | 5.7 | 25.7 | 11.5 | 4.9 | 36.7 | 13.7 | 7.5 | 15 | 15 | 15 | | y4 (1+) | 7.4 | 4.9 | 3.7 | 13.5 | 9.1 | 5.7 | 15.4 | 10.3 | 6.8 | 15 | 15 | 15 | | y5 (1+) | 10.1 | 5.6 | 5.7 | 17.2 | 9.2 | 5.7 | 19.9 | 10.8 | 8.1 | 15 | 15 | 15 | | sum | 9.2 | 4.2 | 3.5 | 14.8 | 8.5 | 4.8 | 17.4 | 9.5 | 5.9 | 15 | 15 | 15 |



Additional Resources and Comments


Assay Details for CPTAC-1393 Collapse assay details

Data source: Panorama

Official Gene Symbol

CLIC1

Peptide Modified Sequence

LHIVQVVC[+57.0]K

Modification Type

Carbamidomethyl Cysteine

Protein - Site of Modification

191

Peptide - Site of Modification

8

Peptide Start

184

Peptide End

192

CPTAC ID

CPTAC-1393

Peptide Molecular Mass

1,094.6270

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

depleted digested plasma

Submitting Laboratory

Broad Institute

Submitting Lab PI

Steven A. Carr


Publication

View Details (opens in a new window)

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18. PMID: 25693799


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Quantiva TSQ

Internal Standard

heavy stable isotope peptide (delta 8-10)

Peptide Standard Purity

>95%

Peptide Standard Label Type

15N

LC

Easy NanoLC1000

Column Packing

Reprosil C18, 1.9um, 200A

Column Dimensions

0.075 x 150 mm

Flow Rate

200 nL/min


Assay Multiplexing Expand assay panel

Broad Institute-Plasma-based Candidate Cancer Biomarkers


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 | | y4 (1+) | 4.3 | 2.6 | 3.2 | 5.4 | 7.7 | 4.7 | 6.9 | 8.1 | 5.7 | 15 | 15 | 15 | | y3 (1+) | 6 | 2.6 | 5.7 | 5.7 | 7.4 | 5.9 | 8.3 | 7.8 | 8.2 | 15 | 15 | 15 | | y2 (1+) | 6.1 | 4.9 | 3.4 | 7.2 | 8.1 | 4.5 | 9.4 | 9.5 | 5.6 | 15 | 15 | 15 | | sum | 4.5 | 2.5 | 2.4 | 4.1 | 7.2 | 3.4 | 6.1 | 7.6 | 4.2 | 15 | 15 | 15 |



Additional Resources and Comments


Assay Details for CPTAC-1394 Collapse assay details

Data source: Panorama

Official Gene Symbol

CLIC1

Peptide Sequence

YLSNAYAR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

209

Peptide End

216

CPTAC ID

CPTAC-1394

Peptide Molecular Mass

956.4716

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

depleted digested plasma

Submitting Laboratory

Broad Institute

Submitting Lab PI

Steven A. Carr


Publication

View Details (opens in a new window)

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18. PMID: 25693799


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Quantiva TSQ

Internal Standard

heavy stable isotope peptide (delta 8-10)

Peptide Standard Purity

>95%

Peptide Standard Label Type

15N

LC

Easy NanoLC1000

Column Packing

Reprosil C18, 1.9um, 200A

Column Dimensions

0.075 x 150 mm

Flow Rate

200 nL/min


Assay Multiplexing Expand assay panel

Broad Institute-Plasma-based Candidate Cancer Biomarkers


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+) | 6.6 | 3.6 | 3.6 | 7.3 | 6.8 | 3.7 | 9.8 | 7.7 | 5.2 | 15 | 15 | 15 | | y6 (1+) | 2.4 | 1.9 | 3.1 | 4.2 | 6.4 | 3.5 | 4.8 | 6.7 | 4.7 | 15 | 15 | 15 | | y5 (1+) | 4.2 | 2.9 | 3.2 | 5 | 7.1 | 3.4 | 6.5 | 7.7 | 4.7 | 15 | 15 | 15 | | sum | 2.2 | 2 | 2.8 | 4 | 6.4 | 3.3 | 4.6 | 6.7 | 4.3 | 15 | 15 | 15 |



Additional Resources and Comments


Assay Details for non-CPTAC-3969 Collapse assay details

Data source: Panorama

Official Gene Symbol

Clic1

Peptide Sequence

NSNPALNDNLEK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

120

Peptide End

131

CPTAC ID

non-CPTAC-3969

Peptide Molecular Mass

1,327.6368

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

>80%

Peptide Standard Label Type

13C and 15N at C-terminus K

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

Broad Institute-Plasma-based Candidate Cancer Biomarkers


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 | | b3 (1+) | 24 | 11.2 | 9.9 | 27.1 | 12.6 | 10.1 | 36.2 | 16.9 | 14.1 | 15 | 15 | 15 | | b2 (1+) | 8.6 | 4 | 5.4 | 14.5 | 6.1 | 6.5 | 16.9 | 7.3 | 8.5 | 15 | 15 | 15 | | y9 (2+) | 20.4 | 10.7 | 8 | 26.7 | 11.4 | 6.9 | 33.6 | 15.6 | 10.6 | 15 | 15 | 15 | | y10 (2+) | 20.1 | 10.3 | 8.8 | 23.1 | 10.7 | 9.6 | 30.6 | 14.9 | 13 | 15 | 15 | 15 | | y9 (1+) | 8.7 | 5.5 | 4.2 | 12 | 6.6 | 6.2 | 14.8 | 8.6 | 7.5 | 15 | 15 | 15 | | sum | 4.4 | 3.9 | 3.2 | 11.9 | 5.1 | 4.8 | 12.7 | 6.4 | 5.8 | 15 | 15 | 15 |



Additional Resources and Comments