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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
TUBB TUBB5
Sequence Length (AA) Molecular Weight (Da)
444 49671
Protein Name
Tubulin beta chain
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY
60 70 80 90 100
YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN
110 120 130 140 150
WAKGHYTEGA ELVDSVLDVV RKEAESCDCL QGFQLTHSLG GGTGSGMGTL
160 170 180 190 200
LISKIREEYP DRIMNTFSVV PSPKVSDTVV EPYNATLSVH QLVENTDETY
210 220 230 240 250
CIDNEALYDI CFRTLKLTTP TYGDLNHLVS ATMSGVTTCL RFPGQLNADL
260 270 280 290 300
RKLAVNMVPF PRLHFFMPGF APLTSRGSQQ YRALTVPELT QQVFDAKNMM
310 320 330 340 350
AACDPRHGRY LTVAAVFRGR MSMKEVDEQM LNVQNKNSSY FVEWIPNNVK
360 370 380 390 400
TAVCDIPPRG LKMAVTFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG
410 420 430 440 444
EGMDEMEFTE AESNMNDLVS EYQQYQDATA EEEEDFGEEA EEEA

Data source: UniProt


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

Uniprot Database Entry PhosphoSitePlus ®

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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-5856 Collapse assay details

Data source: Panorama

Official Gene Symbol
TUBB
Peptide Sequence
ISVYYNEATGGK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
47
Peptide End
58
CPTAC ID
CPTAC-5856
Peptide Molecular Mass
1,300.6299
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
Frozen breast cancer tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG. Clin Chem. 2021 Jun 17:hvab047. doi: 10.1093/clinchem/hvab047. Online ahead of print. PMID: 34136904


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 6500
Internal Standard
peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
10.0 µL/min

Chromatograms

Data source: Panorama


Response Curves

Data source: Panorama

Retrieving Data

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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
y9 (1+) 13.8 7.7 7.8 19.4 20.5 14.3 23.8 21.9 16.3 15 17 15
y7 (1+) 26.2 8.6 7.4 19.6 22.7 14.2 32.7 24.3 16 15 17 15
y10 (1+) 24.3 13.1 5.2 27.4 25.2 10.9 36.6 28.4 12.1 15 17 15
y8 (1+) 14.1 9.3 7.3 20.8 20.8 13.2 25.1 22.8 15.1 15 17 15
sum 13.4 7.3 5.7 17.1 21.1 13.2 21.7 22.3 14.4 15 17 15


Additional Resources and Comments


Assay Details for CPTAC-5881 Collapse assay details

Data source: Panorama

Official Gene Symbol
TUBB
Peptide Sequence
ISVYYNEATGGK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
47
Peptide End
58
CPTAC ID
CPTAC-5881
Peptide Molecular Mass
1,300.6299
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
peptide immunoaffinity
Matrix
FFPE breast cancer tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG. Clin Chem. 2021 Jun 17:hvab047. doi: 10.1093/clinchem/hvab047. Online ahead of print. PMID: 34136904


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 6500
Internal Standard
peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
10.0 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
y8 (1+) 19.4 5 7.6 14.9 11 9.5 24.5 12.1 12.2 12 12 12
y7 (1+) 12.2 5.8 8.4 17.2 12.1 10.2 21.1 13.4 13.2 12 12 12
y9 (1+) 8.6 5.5 6.3 9.4 9.1 9.8 12.7 10.6 11.7 12 12 12
y10 (1+) 19.2 9 5.7 23.2 15.9 12.6 30.1 18.3 13.8 12 12 12
sum 9 4.9 6.4 10.7 10.1 9.7 14 11.2 11.6 12 12 12


Additional Resources and Comments