CD40, CPTAC-5956 - CPTAC Assay Portal | Office of Cancer Clinical Proteomics Research

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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.

Overview Data source: UniProt

Official Gene Symbol	Other Aliases
CD40	TNFRSF5

Sequence Length (AA)	Molecular Weight (Da)
277	30619

Protein Name
Tumor necrosis factor receptor superfamily member 5

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MVRLPLQCVL	WGCLLTAVHP	EPPTACREKQ	YLINSQCCSL	CQPGQKLVSD
60	70	80	90	100
CTEFTETECL	PCGESEFLDT	WNRETHCHQH	KYCDPNLGLR	VQQKGTSETD
110	120	130	140	150
TICTCEEGWH	CTSEACESCV	LHRSCSPGFG	VKQIATGVSD	TICEPCPVGF
160	170	180	190	200
FSNVSSAFEK	CHPWTSCETK	DLVVQQAGTN	KTDVVCGPQD	RLRALVVIPI
210	220	230	240	250
IFGILFAILL	VLVFIKKVAK	KPTNKAPHPK	QEPQEINFPD	DLPGSNTAAP
260	270	277
VQETLHGCQP	VTQEDGKESR	ISVQERQ

Data source: UniProt

Protein Map Collapse protein map

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

Uniprot Database Entry PhosphoSitePlus ®

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Assay Details for CPTAC-5957 Collapse assay details

Data source: Panorama

Official Gene Symbol: CD40
Peptide Modified Sequence: SC[+57.021464]SPGFGVK
Modification Type: Carbamidomethyl (C)
Protein - Site of Modification: N/A
Peptide - Site of Modification: 4
Peptide Start: 124
Peptide End: 132

CPTAC ID: CPTAC-5957
Peptide Molecular Mass: 937.4328
Species: Homo sapiens (Human)
Assay Type: Enrichment MRM
Enrichment Method: peptide immunoaffinity
Matrix: FFPE tumor tissue lysate pool
Submitting Laboratory: Fred Hutchinson Cancer Research Center
Submitting Lab PI: Amanda Paulovich

Publication

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG.Front Immunol. 2021 Nov 11;12:765898. doi: 10.3389/fimmu.2021.765898. eCollection 2021.PMID: 34858420

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument: QTRAP 5500
Internal Standard: peptide
Peptide Standard Purity: >95%
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: 0.3 µL/min

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Repeatability

Data source: Panorama

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	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+)	26.3	20.3	15	20.2	27.8	22.7	33.2	34.4	27.2	13	25	14
y6 (1+)	6.9	4.5	4.7	8.2	8.8	9.7	10.7	9.9	10.8	13	25	14
y7 (1+)	7.1	3.7	3.4	8.5	8.2	9.9	11.1	9	10.5	13	25	14
b3 (1+)	13.1	8.8	6	13.5	9.6	15.1	18.8	13	16.2	13	25	14
b2 (1+)	6.9	3.6	2.6	9.4	8.5	12.5	11.7	9.2	12.8	13	25	14
y8 (2+)	23.6	10.5	5.2	26.7	14.1	12.7	35.6	17.6	13.7	13	25	14
y5 (1+)	13.3	20.6	14.6	18.9	20.8	19.1	23.1	29.3	24	13	25	14
sum	6.3	3.4	3.1	8.5	8.3	10.8	10.6	9	11.2	13	25	14

Additional Resources and Comments

Resources

Download SOPs

View Peptide in Panorama

View Protein in Panorama

View in CPTC Antibody Portal

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