Col3a1, CPTAC-3364 - CPTAC Assay Portal | Office of Cancer Clinical Proteomics Research

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
Col3a1	N/A

Sequence Length (AA)	Molecular Weight (Da)
1464	138943

Protein Name
Collagen alpha-1(III) chain

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MMSFVQSGTW	FLLTLLHPTL	ILAQQSNVDE	LGCSHLGQSY	ESRDVWKPEP
60	70	80	90	100
CQICVCDSGS	VLCDDIICDE	EPLDCPNPEI	PFGECCAICP	QPSTPAPVLP
110	120	130	140	150
DGHGPQGPKG	DPGPPGIPGR	NGDPGLPGQP	GLPGPPGSPG	ICESCPTGGQ
160	170	180	190	200
NYSPQFDSYD	VKSGVGGMGG	YPGPAGPPGP	PGPPGSSGHP	GSPGSPGYQG
210	220	230	240	250
PPGEPGQAGP	AGPPGPPGAL	GPAGPAGKDG	ESGRPGRPGE	RGLPGPPGIK
260	270	280	290	300
GPAGMPGFPG	MKGHRGFDGR	NGEKGETGAP	GLKGENGLPG	DNGAPGPMGP
310	320	330	340	350
RGAPGERGRP	GLPGAAGARG	NDGARGSDGQ	PGPPGPPGTA	GFPGSPGAKG
360	370	380	390	400
EVGPAGSPGS	NGSPGQRGEP	GPQGHAGAQG	PPGPPGNNGS	PGGKGEMGPA
410	420	430	440	450
GIPGAPGLIG	ARGPPGPAGT	NGIPGTRGPS	GEPGKNGAKG	EPGARGERGE
460	470	480	490	500
AGSPGIPGPK	GEDGKDGSPG	EPGANGLPGA	AGERGPSGFR	GPAGPNGIPG
510	520	530	540	550
EKGPPGERGG	PGPAGPRGVA	GEPGRDGTPG	GPGIRGMPGS	PGGPGNDGKP
560	570	580	590	600
GPPGSQGESG	RPGPPGPSGP	RGQPGVMGFP	GPKGNDGAPG	KNGERGGPGG
610	620	630	640	650
PGLPGPAGKN	GETGPQGPPG	PTGPAGDKGD	SGPPGPQGLQ	GIPGTGGPPG
660	670	680	690	700
ENGKPGEPGP	KGEVGAPGAP	GGKGDSGAPG	ERGPPGTAGI	PGARGGAGPP
710	720	730	740	750
GPEGGKGPAG	PPGPPGASGS	PGLQGMPGER	GGPGSPGPKG	EKGEPGGAGA
760	770	780	790	800
DGVPGKDGPR	GPAGPIGPPG	PAGQPGDKGE	GGSPGLPGIA	GPRGGPGERG
810	820	830	840	850
EHGPPGPAGF	PGAPGQNGEP	GAKGERGAPG	EKGEGGPPGP	AGPTGSSGPA
860	870	880	890	900
GPPGPQGVKG	ERGSPGGPGT	AGFPGGRGLP	GPPGNNGNPG	PPGPSGAPGK
910	920	930	940	950
DGPPGPAGNS	GSPGNPGIAG	PKGDAGQPGE	KGPPGAQGPP	GSPGPLGIAG
960	970	980	990	1000
LTGARGLAGP	PGMPGPRGSP	GPQGIKGESG	KPGASGHNGE	RGPPGPQGLP
1010	1020	1030	1040	1050
GQPGTAGEPG	RDGNPGSDGQ	PGRDGSPGGK	GDRGENGSPG	APGAPGHPGP
1060	1070	1080	1090	1100
PGPVGPSGKS	GDRGETGPAG	PSGAPGPAGA	RGAPGPQGPR	GDKGETGERG
1110	1120	1130	1140	1150
SNGIKGHRGF	PGNPGPPGSP	GAAGHQGAIG	SPGPAGPRGP	VGPHGPPGKD
1160	1170	1180	1190	1200
GTSGHPGPIG	PPGPRGNRGE	RGSEGSPGHP	GQPGPPGPPG	APGPCCGGGA
1210	1220	1230	1240	1250
AAIAGVGGEK	SGGFSPYYGD	DPMDFKINTE	EIMSSLKSVN	GQIESLISPD
1260	1270	1280	1290	1300
GSRKNPARNC	RDLKFCHPEL	KSGEYWVDPN	QGCKMDAIKV	FCNMETGETC
1310	1320	1330	1340	1350
INASPMTVPR	KHWWTDSGAE	KKHVWFGESM	NGGFQFSYGP	PDLPEDVVDV
1360	1370	1380	1390	1400
QLAFLRLLSS	RASQNITYHC	KNSIAYMDQA	SGNVKKSLKL	MGSNEGEFKA
1410	1420	1430	1440	1450
EGNSKFTYTV	LEDGCTKHTG	EWSKTVFEYQ	TRKAMRLPII	DIAPYDIGGP
1460	1464
DQEFGVDIGP	VCFL

Data source: UniProt

Protein Map Collapse protein map

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

Uniprot Database Entry PhosphoSitePlus ®

Click a point on a node

to view detailed assay information below

All other points link out to UniProt

Assay Details for CPTAC-1180 Collapse assay details

Data source: Panorama

Official Gene Symbol: COL3A1
Peptide Sequence: GPVGPSGPPGK
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 1140
Peptide End: 1150

CPTAC ID: CPTAC-1180
Peptide Molecular Mass: 948.5029
Species: Homo sapiens (Human)
Assay Type: Direct MRM
Matrix: Ovarian cancer tumor tissue lysate
Submitting Laboratory: Pacific Northwest National Laboratory
Submitting Lab PI: Tao Liu

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument: TSQ Vantage
Internal Standard: peptide
Peptide Standard Purity: >95%
Peptide Standard Label Type: 13C and 15N at C-terminus K

LC: Waters nanoACQUITY (Part Number 176016000)
Column Packing: Waters BEH C18, 1.7 um 130 Å (Part Number 186007485)
Column Dimensions: 100 um x 100 mm
Flow Rate: 0.5 uL/min

Chromatograms

Data source: Panorama

view larger image

Response Curves

Data source: Panorama

view larger image

Retrieving Data

Repeatability

Data source: Panorama

view larger image

	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+)	29	13	14.2	27.5	15.8	14.8	40	20.5	20.5	15	15	15
y7 (1+)	22.9	7.4	9.6	22	15.1	11.7	31.8	16.8	15.1	15	15	15
y8 (1+)	13.1	4.9	8.9	16.2	8.5	8.9	20.8	9.8	12.6	15	15	15
sum	8.9	5.1	6.4	9.2	9.3	7.5	12.8	10.6	9.9	15	15	15

Additional Resources and Comments

Resources

Download SOPs

View Peptide in Panorama

View Protein in Panorama

Comments

Assay Details for non-CPTAC-3364 Collapse assay details

Data source: Panorama

Official Gene Symbol: Col3a1
Peptide Sequence: GGAGPPGPEGGK
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 695
Peptide End: 706

CPTAC ID: non-CPTAC-3364
Peptide Molecular Mass: 979.4723
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.