S100A9, CPTAC-1155 - CPTAC Assay Portal (original) (raw)
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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-1155: View additional DLQNFLK data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MTCKMSQLER | NIETIINTFH | QYSVKLGHPD | TLNQGEFKEL | VRKDLQNFLK |
| 60 | 70 | 80 | 90 | 100 |
| KENKNEKVIE | HIMEDLDTNA | DKQLSFEEFI | MLMARLTWAS | HEKMHEGDEG |
| 110 | 114 | |||
| PGHHHKPGLG | EGTP |
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-1295 Collapse assay details
Data source: Panorama
Official Gene Symbol
S100A9
Peptide Sequence
LGHPDTLNQGEFK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
26
Peptide End
38
CPTAC ID
CPTAC-1295
Peptide Molecular Mass
1,454.7154
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Human serum digest
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
LCMS-8040
Internal Standard
Stable isotope-labeled peptides
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C at C-terminus K
LC
Nexera X2 UHPLC
Column Packing
C18, 3 µm, 300 Å
Column Dimensions
1.0 mm I.D. x 15 cm
Flow Rate
50 µL/min
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 |
| b3 (1+) | 14 | 1.9 | 1.6 | 19.6 | 2 | 1.7 | 24.1 | 2.8 | 2.3 | 15 | 15 | 15 |
| y5 (1+) | 15 | 4 | 2.9 | 18 | 3.8 | 2.8 | 23.4 | 5.5 | 4 | 15 | 15 | 15 |
| y6 (1+) | 16.1 | 2 | 2.1 | 21.1 | 2.2 | 2.3 | 26.5 | 3 | 3.1 | 15 | 15 | 15 |
| sum | 14.7 | 1.1 | 1.4 | 19.6 | 1 | 1.4 | 24.5 | 1.5 | 2 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-1294 Collapse assay details
Data source: Panorama
Official Gene Symbol
S100A9
Peptide Sequence
NIETIINTFHQYSVK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
11
Peptide End
25
CPTAC ID
CPTAC-1294
Peptide Molecular Mass
1,805.9312
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Human serum digest
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
LCMS-8040
Internal Standard
Stable isotope-labeled peptides
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C at C-terminus K
LC
Nexera X2 UHPLC
Column Packing
C18, 3 µm, 300 Å
Column Dimensions
1.0 mm I.D. x 15 cm
Flow Rate
50 µL/min
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 |
| y10 (2+) | 44.2 | 6.1 | 2.9 | 71.1 | 8.6 | 4.4 | 83.7 | 10.5 | 5.3 | 15 | 15 | 15 |
| y12 (2+) | 41.6 | 5.6 | 3.1 | 66.9 | 5 | 4.9 | 78.8 | 7.5 | 5.8 | 15 | 15 | 15 |
| y13 (2+) | 40.5 | 2.2 | 1.8 | 65.2 | 2.3 | 1.1 | 76.8 | 3.2 | 2.1 | 15 | 15 | 15 |
| sum | 40.1 | 1.5 | 1.5 | 65.5 | 1.9 | 0.8 | 76.8 | 2.4 | 1.7 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-1155 Collapse assay details
Data source: Panorama
Official Gene Symbol
S100A9
Peptide Sequence
DLQNFLK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
44
Peptide End
50
CPTAC ID
non-CPTAC-1155
Peptide Molecular Mass
876.4705
Species
Homo sapiens (Human)
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
6490 Triple Quad (Agilent)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
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
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 |
| b5 (1+) | 52 | 18.5 | 7.5 | 45.5 | 20.8 | 9.4 | 69.1 | 27.8 | 12 | 13 | 14 | 15 |
| b3 (1+) | 25.9 | 13.4 | 10.8 | 47.7 | 14.4 | 12 | 54.3 | 19.7 | 16.1 | 10 | 15 | 15 |
| y3 (1+) | 16.5 | 7.2 | 7.1 | 23.3 | 9.8 | 8.9 | 28.6 | 12.2 | 11.4 | 12 | 15 | 15 |
| y4 (1+) | 14.1 | 6.2 | 7.7 | 30.8 | 5.8 | 8 | 33.9 | 8.5 | 11.1 | 15 | 15 | 15 |
| y5 (1+) | 8.4 | 8.5 | 5.5 | 11.7 | 11.7 | 7 | 14.4 | 14.5 | 8.9 | 15 | 15 | 15 |
| sum | 9.5 | 6.8 | 4.3 | 13.6 | 9.2 | 4.5 | 16.6 | 11.4 | 6.2 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-3410 Collapse assay details
Data source: Panorama
Official Gene Symbol
S100a9
Peptide Sequence
SITTIIDTFHQYSR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
12
Peptide End
25
CPTAC ID
non-CPTAC-3410
Peptide Molecular Mass
1,680.8471
Species
Mus musculus (Mouse)
Assay Type
Direct MRM
Matrix
Plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Publication
View Details (opens in a new window)
Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays. Michaud SA, Sinclair NJ, Petrošová H, Palmer AL, Pistawka AJ, Zhang S, Hardie DB, Mohammed Y Eshghi A1, Richard VR, Sickmann A, Borchers CH. Commun Biol. 2018 Jun 27;1:78. doi: 10.1038/s42003-018-0087-6. eCollection 2018.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Agilent 6490/6495 QQQ
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
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
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 |
| y12 (3+) | 6.1 | 3.4 | 4.8 | 12.3 | 7.1 | 5.3 | 13.7 | 7.9 | 7.2 | 15 | 15 | 15 |
| y9 (2+) | 6.5 | 6.3 | 3.3 | 15.7 | 4.5 | 4.8 | 17 | 7.7 | 5.8 | 15 | 15 | 15 |
| y10 (2+) | 4.9 | 3.5 | 5.3 | 14.6 | 6.1 | 6.7 | 15.4 | 7 | 8.5 | 15 | 15 | 15 |
| y11 (2+) | 4.9 | 3.1 | 3.4 | 13.4 | 9.8 | 4.2 | 14.3 | 10.3 | 5.4 | 15 | 15 | 15 |
| y12 (2+) | 5.1 | 3.4 | 5.6 | 17.3 | 7 | 5.4 | 18 | 7.8 | 7.8 | 15 | 15 | 15 |
| sum | 4 | 3 | 3.6 | 15.7 | 5.8 | 3.4 | 16.2 | 6.5 | 5 | 15 | 15 | 15 |