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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.

Overview Data source: UniProt

Official Gene Symbol Other Aliases
Pdlim1 Clim1
Sequence Length (AA) Molecular Weight (Da)
327 35774
Protein Name
PDZ and LIM domain protein 1
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MTTQQIVLQG PGPWGFRLVG GKDFEQPLAI SRVTPGSKAA IANLCIGDLI
60 70 80 90 100
TAIDGEDTSS MTHLEAQNKI KGCADNMTLT VSRSEQKIWS PLVTEEGKRH
110 120 130 140 150
PYKMNLASEP QEVLHIGSAH NRSAMPFTAS PAPSTRVITN QYNSPTGLYS
160 170 180 190 200
SENISNFNNA VESKTSASGE EANSRPVVQP HPSGSLIIDK DSEVYKMLQE
210 220 230 240 250
KQELNEPPKQ STSFLVLQEI LESDGKGDPN KPSGFRSVKA PVTKVAASVG
260 270 280 290 300
NAQKLPICDK CGTGIVGVFV KLRDHHRHPE CYVCTDCGIN LKQKGHFFVE
310 320 327
DQIYCEKHAR ERVTPPEGYD VVTVFRE

Data source: UniProt


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

Uniprot Database Entry PhosphoSitePlus ®

Click a point on a node
to view detailed assay information below
All other points link out to UniProt



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

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
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

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
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

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
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

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
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

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
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


Additional Resources and Comments