PDIA4, CPTAC-105 - 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
PDIA4	ERP70, ERP72

Sequence Length (AA)	Molecular Weight (Da)
645	72932

Protein Name
Protein disulfide-isomerase A4

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MRPRKAFLLL	LLLGLVQLLA	VAGAEGPDED	SSNRENAIED	EEEEEEEDDD
60	70	80	90	100
EEEDDLEVKE	ENGVLVLNDA	NFDNFVADKD	TVLLEFYAPW	CGHCKQFAPE
110	120	130	140	150
YEKIANILKD	KDPPIPVAKI	DATSASVLAS	RFDVSGYPTI	KILKKGQAVD
160	170	180	190	200
YEGSRTQEEI	VAKVREVSQP	DWTPPPEVTL	VLTKENFDEV	VNDADIILVE
210	220	230	240	250
FYAPWCGHCK	KLAPEYEKAA	KELSKRSPPI	PLAKVDATAE	TDLAKRFDVS
260	270	280	290	300
GYPTLKIFRK	GRPYDYNGPR	EKYGIVDYMI	EQSGPPSKEI	LTLKQVQEFL
310	320	330	340	350
KDGDDVIIIG	VFKGESDPAY	QQYQDAANNL	REDYKFHHTF	STEIAKFLKV
360	370	380	390	400
SQGQLVVMQP	EKFQSKYEPR	SHMMDVQGST	QDSAIKDFVL	KYALPLVGHR
410	420	430	440	450
KVSNDAKRYT	RRPLVVVYYS	VDFSFDYRAA	TQFWRSKVLE	VAKDFPEYTF
460	470	480	490	500
AIADEEDYAG	EVKDLGLSES	GEDVNAAILD	ESGKKFAMEP	EEFDSDTLRE
510	520	530	540	550
FVTAFKKGKL	KPVIKSQPVP	KNNKGPVKVV	VGKTFDSIVM	DPKKDVLIEF
560	570	580	590	600
YAPWCGHCKQ	LEPVYNSLAK	KYKGQKGLVI	AKMDATANDV	PSDRYKVEGF
610	620	630	640	645
PTIYFAPSGD	KKNPVKFEGG	DRDLEHLSKF	IEEHATKLSR	TKEEL

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-105 Collapse assay details

Data source: Panorama

Official Gene Symbol: PDIA4
Peptide Sequence: IDATSASVLASR
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 120
Peptide End: 131

CPTAC ID: CPTAC-105
Peptide Molecular Mass: 1,189.6303
Species: Homo sapiens (Human)
Assay Type: Direct MRM
Matrix: cell line lysate pool
Submitting Laboratory: Fred Hutchinson Cancer Research Center
Submitting Lab PI: Amanda Paulovich

Publication

View Details (opens in a new window)

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

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
y8 (1+)	7.7	5.8	3.3	6.9	7.1	4.3	10.3	9.2	5.4	15	25	15
y7 (1+)	8.4	7	3.8	7.9	7.7	4.7	11.5	10.4	6	15	25	15
y6 (1+)	10.3	6.3	3.5	12.9	6.7	6.1	16.5	9.2	7	15	25	15
sum	6.1	4.9	3.3	7.4	5.8	4.2	9.6	7.6	5.3	15	25	15

Selectivity

Data source: Panorama

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	Slope of Curve Fit for cell line
fragment_ion	HCC1187	HCC1419	HCC1954	HCC70	MCF12A	MDAMB175VII	ZR751	ZR7530
y8 (1+)	-0.02	-0.31	-0.04	-0.04	-0.09	-0.06	-0.1	-0.07
y6 (1+)	-0.04	-0.32	-0.04	-0.04	-0.09	-0.07	-0.1	-0.07
y7 (1+)	-0.03	-0.31	-0.04	-0.04	-0.09	-0.07	-0.12	-0.08
sum	-0.03	-0.31	-0.04	-0.04	-0.09	-0.07	-0.1	-0.07

Stability

Data source: Panorama

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Fragment ion / Transition	control_intra_CV	actual_temp_intra_CV	frozen_intra_CV	FTx1_intra_CV	FTx2_intra_CV
y8 (1+)	3.6	3.7	3.9	NA	2.2
y6 (1+)	2.1	3.6	0.8	NA	5.9
y7 (1+)	4.3	3.8	3.5	NA	6.1
sum	1.5	2.3	1.2	NA	1.1

Fragment ion / Transition	all_intra_CV	all_inter_CV
y8 (1+)	3.4	3.5
y6 (1+)	3.2	2.8
y7 (1+)	4.3	4.6
sum	1.7	1.7

Endogenous

Data source: Panorama

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Fragment ion / Transition	intra_CV	inter_CV	total_CV
y7 (1+)	6.9	8	10.6
y6 (1+)	6.4	6.8	9.3
y8 (1+)	5.9	7.2	9.3
sum	4.9	5.8	7.6

Additional Resources and Comments

Resources

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View Peptide in Panorama

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