B2M, CPTAC-1232 - 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
CPTAC-6233: View additional VNHVTLSQPK data
CPTAC-1232: View additional VEHSDLSFSK data
non-CPTAC-3965: View additional TPQIQVYSR data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MSRSVALAVL | ALLSLSGLEA | IQRTPKIQVY | SRHPAENGKS | NFLNCYVSGF |
| 60 | 70 | 80 | 90 | 100 |
| HPSDIEVDLL | KNGERIEKVE | HSDLSFSKDW | SFYLLYYTEF | TPTEKDEYAC |
| 110 | 119 | |||
| RVNHVTLSQP | KIVKWDRDM |
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-6233 Collapse assay details
Data source: Panorama
Official Gene Symbol
B2M
Peptide Sequence
VNHVTLSQPK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
7
Peptide Start
102
Peptide End
111
CPTAC ID
CPTAC-6233
Peptide Molecular Mass
1,121.6193
Species
Homo Sapiens
Assay Type
Enrichment MRM or SRM
Enrichment Method
N/A
Matrix
Frozen tissue
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
QTRAP 5500
Internal Standard
Extended heavy peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent
Column Packing
Reprosil C18, 3um
Column Dimensions
75µm x 15cm
Flow Rate
0.3 µL/min
Assay Multiplexing Expand assay panel
Pacific Northwest National Laboratory-DirectMRM2
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 |
| y4 (1+) | 4.2 | 1.4 | 14.3 | 5.5 | 4.3 | 16.9 | 6.9 | 4.5 | 22.1 | 15 | 15 | 15 |
| b5 (1+) | 6.4 | 3 | 2.1 | 5.6 | 4.8 | 3.8 | 8.5 | 5.7 | 4.3 | 15 | 15 | 14 |
| b4 (1+) | 9.2 | 3.3 | 8.6 | 11.5 | 6.1 | 10 | 14.7 | 6.9 | 13.2 | 15 | 15 | 15 |
| y5 (1+) | 3.7 | 3 | 7.2 | 4.8 | 4 | 10 | 6.1 | 5 | 12.3 | 15 | 15 | 15 |
| y8 (2+) | 8.4 | 3.7 | 7.3 | 11.6 | 4.9 | 7.9 | 14.3 | 6.1 | 10.8 | 15 | 15 | 15 |
| sum | 2.9 | 1.7 | 6.6 | 3.4 | 3.9 | 9 | 4.5 | 4.3 | 11.2 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-1232 Collapse assay details
Data source: Panorama
Official Gene Symbol
B2M
Peptide Sequence
VEHSDLSFSK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
69
Peptide End
78
CPTAC ID
CPTAC-1232
Peptide Molecular Mass
1,147.5510
Species
Homo sapiens (Human)
Assay Type
Direct MRM or SRM
Matrix
Ovarian cancer tumor tissue lysate
Submitting Laboratory
Pacific Northwest National Laboratory
Submitting Lab PI
Tao Liu
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
TSQ Vantage
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Waters nanoACQUITY (Part Number 176016000)
Column Packing
Waters BEH C18, 1.7 um 130 Å (Part Number 186007485)
Column Dimensions
100 um x 100 mm
Flow Rate
0.5 uL/min
Assay Multiplexing Expand assay panel
Pacific Northwest National Laboratory-DirectMRM2
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 |
| y3 (1+) | 21.9 | 5.7 | 9.2 | 22.1 | 9.5 | 12.8 | 31.1 | 11.1 | 15.8 | 15 | 15 | 15 |
| y5 (1+) | 29.4 | 7.9 | 15.2 | 32.5 | 8.7 | 17.5 | 43.8 | 11.8 | 23.2 | 15 | 15 | 15 |
| y7 (1+) | 36.9 | 14.8 | 9.2 | 34.7 | 16 | 10.5 | 50.7 | 21.8 | 14 | 15 | 15 | 15 |
| sum | 16 | 6.8 | 9.7 | 16 | 9.9 | 12.3 | 22.6 | 12 | 15.7 | 15 | 15 | 15 |
Selectivity
Data source: Panorama
| Slope of Curve Fit for cell line | ||||||
|---|---|---|---|---|---|---|
| fragment_ion | 1 | 2 | 3 | 4 | 5 | 6 |
| y5 (1+) | 1.63 | 1.69 | 1.93 | 1.4 | 1.72 | 1.66 |
| y7 (1+) | 1.48 | 1.59 | 1.85 | 1.44 | 1.66 | 1.55 |
| y3 (1+) | 1.52 | 1.71 | 1.66 | 1.3 | 1.72 | 1.22 |
| sum | 1.53 | 1.68 | 1.74 | 1.35 | 1.7 | 1.35 |
Stability
Data source: Panorama
| Fragment ion / Transition | control_intra_CV | actual_temp_intra_CV | frozen_intra_CV | FTx1_intra_CV | FTx2_intra_CV |
|---|---|---|---|---|---|
| y3 (1+) | 5.9 | 16.1 | 3.8 | 12.3 | 10.4 |
| y5 (1+) | 5 | 12.4 | 10.8 | 1.7 | 9.8 |
| y7 (1+) | 8.1 | 19.1 | 3.9 | 5 | 3.1 |
| sum | 3.4 | 12.5 | 2.1 | 5.8 | 6.9 |
| Fragment ion / Transition | all_intra_CV | all_inter_CV |
|---|---|---|
| y3 (1+) | 10.8 | 12.8 |
| y5 (1+) | 8.7 | 7.8 |
| y7 (1+) | 9.7 | 11.4 |
| sum | 7.2 | 9.6 |
Endogenous
Data source: Panorama
| Fragment ion / Transition | intra_CV | inter_CV | total_CV |
|---|---|---|---|
| y3 (1+) | 34.7 | 38.4 | 51.8 |
| y7 (1+) | 30.8 | 53.5 | 61.7 |
| y5 (1+) | 39.6 | 54.6 | 67.4 |
| sum | 27.3 | 41.1 | 49.3 |
Additional Resources and Comments
Assay Details for non-CPTAC-3965 Collapse assay details
Data source: Panorama
Official Gene Symbol
B2m
Peptide Sequence
TPQIQVYSR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
24
Peptide End
32
CPTAC ID
non-CPTAC-3965
Peptide Molecular Mass
1,090.5771
Species
Mus musculus (Mouse)
Assay Type
Direct MRM or SRM
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
>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
Pacific Northwest National Laboratory-DirectMRM2
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 |
| y6 (1+) | 12.3 | 7.3 | 5.9 | 15.1 | 12.5 | 7.9 | 19.5 | 14.5 | 9.9 | 15 | 15 | 15 |
| y7 (1+) | 10.6 | 8.5 | 3.2 | 10.5 | 10.6 | 5.7 | 14.9 | 13.6 | 6.5 | 15 | 15 | 15 |
| y8 (2+) | 10.3 | 5.3 | 5.7 | 9.6 | 5.6 | 6.6 | 14.1 | 7.7 | 8.7 | 15 | 15 | 15 |
| y4 (1+) | 21.7 | 6.6 | 3.9 | 27.2 | 7.1 | 5.3 | 34.8 | 9.7 | 6.6 | 15 | 15 | 15 |
| y5 (1+) | 12.4 | 4.7 | 4.6 | 13.5 | 6 | 5.6 | 18.3 | 7.6 | 7.2 | 15 | 15 | 15 |
| sum | 3.6 | 3.2 | 2.9 | 5.6 | 5 | 4.1 | 6.7 | 5.9 | 5 | 15 | 15 | 15 |