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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
Cx3cl1 Cx3c, Fkn, Scyd1
Sequence Length (AA) Molecular Weight (Da)
395 42099
Protein Name
Fractalkine
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MAPSPLAWLL RLAAFFHLCT LLPGQHLGMT KCEIMCDKMT SRIPVALLIR
60 70 80 90 100
YQLNQESCGK RAIVLETTQH RRFCADPKEK WVQDAMKHLD HQAAALTKNG
110 120 130 140 150
GKFEKRVDNV TPGITLATRG LSPSALTKPE SATLEDLALE LTTISQEARG
160 170 180 190 200
TMGTSQEPPA AVTGSSLSTS EAQDAGLTAK PQSIGSFEAA DISTTVWPSP
210 220 230 240 250
AVYQSGSSSW AEEKATESPS TTAPSPQVST TSPSTPEENV GSEGQPPWVQ
260 270 280 290 300
GQDLSPEKSL GSEEINPVHT DNFQERGPGN TVHPSVAPIS SEETPSPELV
310 320 330 340 350
ASGSQAPKIE EPIHATADPQ KLSVLITPVP DTQAATRRQA VGLLAFLGLL
360 370 380 390 395
FCLGVAMFAY QSLQGCPRKM AGEMVEGLRY VPRSCGSNSY VLVPV

Data source: UniProt


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

Uniprot Database Entry PhosphoSitePlus ®

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All other points link out to UniProt



Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-5967 Collapse assay details

Data source: Panorama

Official Gene Symbol
CX3CL1
Peptide Sequence
ALGTSPELPTGVTGSSGTR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
150
Peptide End
168
CPTAC ID
CPTAC-5967
Peptide Molecular Mass
1,786.9061
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
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 R
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


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
b7 (1+) 9.6 12.3 10.3 11.3 15.2 16.8 14.8 19.6 19.7 13 25 14
y7 (1+) 6.8 9 4 10 12 14.3 12.1 15 14.8 13 25 14
y9 (1+) 27.1 14.8 8.3 27.2 19.3 14.7 38.4 24.3 16.9 13 25 14
y11 (1+) 4.1 5.6 3.1 6.2 11.2 10.6 7.4 12.5 11 13 25 14
y12 (1+) 14.6 7.2 6.7 17.4 13.2 14 22.7 15 15.5 13 25 14
b8 (1+) 5 7.5 4.8 9.8 11.3 12.1 11 13.6 13 13 25 14
y6 (1+) 17.6 13.1 13.9 17.7 17.4 19.1 25 21.8 23.6 13 25 14
sum 3.7 5.2 2.7 6.8 11.1 11.3 7.7 12.3 11.6 13 25 14


Additional Resources and Comments


Assay Details for non-CPTAC-3612 Collapse assay details

Data source: Panorama

Official Gene Symbol
Cx3cl1
Peptide Sequence
SLGSEEINPVHTDNFQER
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
259
Peptide End
276
CPTAC ID
non-CPTAC-3612
Peptide Molecular Mass
2,070.9607
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

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
b2 (1+) 8.8 4.6 6.2 11.5 7.8 7.3 14.5 9.1 9.6 15 15 15
y12 (2+) 18.2 6.3 7.8 19.7 10.3 8.6 26.8 12.1 11.6 15 15 15
y13 (2+) 18.2 10.3 9.6 26.8 10.8 9.8 32.4 14.9 13.7 15 15 15
y14 (2+) 20.9 11.7 7.1 18.6 14.1 8.3 28 18.3 10.9 15 15 15
y16 (2+) 7.4 5.2 5.3 6.5 7.7 5.5 9.8 9.3 7.6 15 15 15
sum 3.7 3 3.1 6.1 7 3.9 7.1 7.6 5 15 15 15


Additional Resources and Comments