CKAP4, CPTAC-336 - 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
CKAP4	N/A

Sequence Length (AA)	Molecular Weight (Da)
602	66022

Protein Name
Cytoskeleton-associated protein 4

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MPSAKQRGSK	GGHGAASPSE	KGAHPSGGAD	DVAKKPPPAP	QQPPPPPAPH
60	70	80	90	100
PQQHPQQHPQ	NQAHGKGGHR	GGGGGGGKSS	SSSSASAAAA	AAAASSSASC
110	120	130	140	150
SRRLGRALNF	LFYLALVAAA	AFSGWCVHHV	LEEVQQVRRS	HQDFSRQREE
160	170	180	190	200
LGQGLQGVEQ	KVQSLQATFG	TFESILRSSQ	HKQDLTEKAV	KQGESEVSRI
210	220	230	240	250
SEVLQKLQNE	ILKDLSDGIH	VVKDARERDF	TSLENTVEER	LTELTKSIND
260	270	280	290	300
NIAIFTEVQK	RSQKEINDMK	AKVASLEESE	GNKQDLKALK	EAVKEIQTSA
310	320	330	340	350
KSREWDMEAL	RSTLQTMESD	IYTEVRELVS	LKQEQQAFKE	AADTERLALQ
360	370	380	390	400
ALTEKLLRSE	ESVSRLPEEI	RRLEEELRQL	KSDSHGPKED	GGFRHSEAFE
410	420	430	440	450
ALQQKSQGLD	SRLQHVEDGV	LSMQVASARQ	TESLESLLSK	SQEHEQRLAA
460	470	480	490	500
LQGRLEGLGS	SEADQDGLAS	TVRSLGETQL	VLYGDVEELK	RSVGELPSTV
510	520	530	540	550
ESLQKVQEQV	HTLLSQDQAQ	AARLPPQDFL	DRLSSLDNLK	ASVSQVEADL
560	570	580	590	600
KMLRTAVDSL	VAYSVKIETN	ENNLESAKGL	LDDLRNDLDR	LFVKVEKIHE
602
KV

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-335 Collapse assay details

Data source: Panorama

Official Gene Symbol: CKAP4
Peptide Sequence: LEGLGSSEADQDGLASTVR
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 455
Peptide End: 473

CPTAC ID: CPTAC-335
Peptide Molecular Mass: 1,903.9123
Species: Homo sapiens (Human)
Assay Type: Direct MRM
Matrix: cell line lysate pool
Submitting Laboratory: Broad Institute and FHCRC
Submitting Lab PI: Steve Carr

Publication

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Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253

Response curves acquired at Broad Institute. Repeatability data acquired at Fred Hutchinson Cancer Research Center.

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument: 5500 QTRAP (ABSCIEX)
Internal Standard: peptide
Peptide Standard Purity: >95%
Peptide Standard Label Type: 13C,15N

LC: nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing: ChromXP C18-CL, 3 um, 120A
Column Dimensions: 150 x 0.075 mm
Flow Rate: 500 nL / 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
y11 (1+)	9.2	6.6	4.9	15.2	12.8	7.2	17.8	14.4	8.7	15	25	15
y10 (1+)	12.9	10.9	8.9	13.9	11.3	13.1	19	15.7	15.8	15	25	15
y8 (1+)	16.9	8.3	8.4	21.7	9.2	6.9	27.5	12.4	10.9	15	25	15
sum	7.3	6.1	4.5	11	9.2	5.7	13.2	11	7.3	15	25	15

Additional Resources and Comments

Resources

Download SOPs

View Peptide in Panorama

View Protein in Panorama

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