PDLIM1, CPTAC-1441 - 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-1444: View additional DFEQPLAISR data
non-CPTAC-3992: View additional DFEQPLAISR data
CPTAC-1442: View additional VAASIGNAQK data
CPTAC-1443: View additional VWSPLVTEEGK data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MTTQQIDLQG | PGPWGFRLVG | GKDFEQPLAI | SRVTPGSKAA | LANLCIGDVI |
| 60 | 70 | 80 | 90 | 100 |
| TAIDGENTSN | MTHLEAQNRI | KGCTDNLTLT | VARSEHKVWS | PLVTEEGKRH |
| 110 | 120 | 130 | 140 | 150 |
| PYKMNLASEP | QEVLHIGSAH | NRSAMPFTAS | PASSTTARVI | TNQYNNPAGL |
| 160 | 170 | 180 | 190 | 200 |
| YSSENISNFN | NALESKTAAS | GVEANSRPLD | HAQPPSSLVI | DKESEVYKML |
| 210 | 220 | 230 | 240 | 250 |
| QEKQELNEPP | KQSTSFLVLQ | EILESEEKGD | PNKPSGFRSV | KAPVTKVAAS |
| 260 | 270 | 280 | 290 | 300 |
| IGNAQKLPMC | DKCGTGIVGV | FVKLRDRHRH | PECYVCTDCG | TNLKQKGHFF |
| 310 | 320 | 329 | ||
| VEDQIYCEKH | ARERVTPPEG | YEVVTVFPK |
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-1441 Collapse assay details
Data source: Panorama
Official Gene Symbol
PDLIM1
Peptide Modified Sequence
C[+57.0]GTGIVGVFVK
Modification Type
Carbamidomethyl Cysteine
Protein - Site of Modification
263
Peptide - Site of Modification
1
Peptide Start
263
Peptide End
273
CPTAC ID
CPTAC-1441
Peptide Molecular Mass
1,135.6060
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
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV
| n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 34.5 | 15 | 10.4 | 41.4 | 19.8 | 10.2 | 53.9 | 24.8 | 14.6 | 15 | 15 | 15 |
| y10 (2+) | 60.9 | 8.4 | 7.9 | 63.4 | 10.5 | 12.3 | 87.9 | 13.4 | 14.6 | 15 | 15 | 15 |
| y8 (1+) | 5.6 | 2.5 | 3 | 8.2 | 5.9 | 4.7 | 9.9 | 6.4 | 5.6 | 15 | 15 | 15 |
| sum | 5 | 2.6 | 2.8 | 7.8 | 5.8 | 4.4 | 9.3 | 6.4 | 5.2 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-1444 Collapse assay details
Data source: Panorama
Official Gene Symbol
PDLIM1
Peptide Sequence
DFEQPLAISR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
23
Peptide End
32
CPTAC ID
CPTAC-1444
Peptide Molecular Mass
1,174.5982
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
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y7 (1+) | 4.8 | 2.5 | 3.2 | 7.2 | 6.6 | 3.8 | 8.7 | 7.1 | 5 | 15 | 15 | 15 |
| y4 (1+) | 4.8 | 1.9 | 1.7 | 9.2 | 6.1 | 3.5 | 10.4 | 6.4 | 3.9 | 15 | 15 | 15 |
| y6 (1+) | 2.7 | 1.7 | 2.1 | 6.4 | 6.1 | 3.5 | 6.9 | 6.3 | 4.1 | 15 | 15 | 15 |
| sum | 2.1 | 1.5 | 1.9 | 6.4 | 6.1 | 3.4 | 6.7 | 6.3 | 3.9 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-1442 Collapse assay details
Data source: Panorama
Official Gene Symbol
PDLIM1
Peptide Sequence
VAASIGNAQK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
247
Peptide End
256
CPTAC ID
CPTAC-1442
Peptide Molecular Mass
957.5243
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
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 2.5 | 2 | 2.5 | 3.4 | 7 | 3.9 | 4.2 | 7.3 | 4.6 | 15 | 15 | 15 |
| y8 (1+) | 4.3 | 2.8 | 2.7 | 5 | 7.3 | 4 | 6.6 | 7.8 | 4.8 | 15 | 15 | 15 |
| y7 (1+) | 6.6 | 2.8 | 2.4 | 7 | 7.5 | 3.3 | 9.6 | 8 | 4.1 | 15 | 15 | 15 |
| sum | 2.2 | 2.2 | 2.3 | 3.7 | 7.1 | 3.7 | 4.3 | 7.4 | 4.4 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-1443 Collapse assay details
Data source: Panorama
Official Gene Symbol
PDLIM1
Peptide Sequence
VWSPLVTEEGK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
88
Peptide End
98
CPTAC ID
CPTAC-1443
Peptide Molecular Mass
1,243.6449
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
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 4.4 | 2.2 | 2.5 | 6.9 | 5.9 | 5.1 | 8.2 | 6.3 | 5.7 | 15 | 15 | 15 |
| y8 (1+) | 2.9 | 1.4 | 2.1 | 6.1 | 6.8 | 4.3 | 6.8 | 6.9 | 4.8 | 15 | 15 | 15 |
| y9 (1+) | 3 | 1.8 | 1.6 | 5.2 | 6.3 | 4.1 | 6 | 6.6 | 4.4 | 15 | 15 | 15 |
| sum | 1.8 | 1.2 | 1.8 | 5.2 | 6.3 | 4.3 | 5.5 | 6.4 | 4.7 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-3992 Collapse assay details
Data source: Panorama
Official Gene Symbol
Pdlim1
Peptide Sequence
DFEQPLAISR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
23
Peptide End
32
CPTAC ID
non-CPTAC-3992
Peptide Molecular Mass
1,174.5982
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 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
Broad Institute-Plasma-based Candidate Cancer Biomarkers
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| b4 (1+) | 6.5 | 3.1 | 2.2 | 7.5 | 4.8 | 6.5 | 9.9 | 5.7 | 6.9 | 15 | 15 | 15 |
| b2 (1+) | 9.6 | 3.6 | 2.9 | 10.6 | 4.1 | 5 | 14.3 | 5.5 | 5.8 | 15 | 15 | 15 |
| y2 (1+) | 5.9 | 2.5 | 3.8 | 8.4 | 5.2 | 4.4 | 10.3 | 5.8 | 5.8 | 15 | 15 | 15 |
| y6 (1+) | 6.6 | 2.7 | 3 | 12.2 | 3.6 | 4.1 | 13.9 | 4.5 | 5.1 | 15 | 15 | 15 |
| y7 (1+) | 10.7 | 4.2 | 2.9 | 14.4 | 4.2 | 3.5 | 17.9 | 5.9 | 4.5 | 15 | 15 | 15 |
| sum | 3.8 | 1.3 | 1.3 | 7.7 | 3 | 3.6 | 8.6 | 3.3 | 3.8 | 15 | 15 | 15 |