VIM, CPTAC-1303 - 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
VIM	N/A

Sequence Length (AA)	Molecular Weight (Da)
466	53652

Protein Name
Vimentin

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MSTRSVSSSS	YRRMFGGPGT	ASRPSSSRSY	VTTSTRTYSL	GSALRPSTSR
60	70	80	90	100
SLYASSPGGV	YATRSSAVRL	RSSVPGVRLL	QDSVDFSLAD	AINTEFKNTR
110	120	130	140	150
TNEKVELQEL	NDRFANYIDK	VRFLEQQNKI	LLAELEQLKG	QGKSRLGDLY
160	170	180	190	200
EEEMRELRRQ	VDQLTNDKAR	VEVERDNLAE	DIMRLREKLQ	EEMLQREEAE
210	220	230	240	250
NTLQSFRQDV	DNASLARLDL	ERKVESLQEE	IAFLKKLHEE	EIQELQAQIQ
260	270	280	290	300
EQHVQIDVDV	SKPDLTAALR	DVRQQYESVA	AKNLQEAEEW	YKSKFADLSE
310	320	330	340	350
AANRNNDALR	QAKQESTEYR	RQVQSLTCEV	DALKGTNESL	ERQMREMEEN
360	370	380	390	400
FAVEAANYQD	TIGRLQDEIQ	NMKEEMARHL	REYQDLLNVK	MALDIEIATY
410	420	430	440	450
RKLLEGEESR	ISLPLPNFSS	LNLRETNLDS	LPLVDTHSKR	TLLIKTVETR
460	466
DGQVINETSQ	HHDDLE

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-1018 Collapse assay details

Data source: Panorama

Official Gene Symbol: VIM
Peptide Modified Sequence: ETNLDS[+80.0]LPLVDTHSK
Modification Type: Phospho (ST)
Protein - Site of Modification: 430
Peptide - Site of Modification: 6
Peptide Start: 425
Peptide End: 439

CPTAC ID: CPTAC-1018
Peptide Molecular Mass: 1,747.8030
Species: Homo sapiens (Human)
Assay Type: Enrichment MRM
Enrichment Method: N/A
Matrix: cell lysate
Submitting Laboratory: Fred Hutchinson Cancer Research Center
Submitting Lab PI: Amanda Paulovich

Publication

View Details (opens in a new window)

Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich U, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG. Immobilized metal affinity chromatography coupled to multiple reaction monitoring enables reproducible quantification of phospho-signaling. Molecular and Cellular Proteomics. mcp.O115.054940

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument: QTrap 5500 (Sciex)
Internal Standard: synthetic peptide
Peptide Standard Purity: Crude
Peptide Standard Label Type: 13C and 15N at C-terminus K

LC: nanoLC-2D (Eksigent)
Column Packing: ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions: 75 µm x 15cm
Flow Rate: 300 nL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

CPTAC-1297: SUN1. TLSPTGN[+1.0]ISSAPK	CPTAC-1298: COLGALT1. TALWVATDHNM[+16.0]DN[+1.0]TSTVLR	CPTAC-1299: APOB. FN[+1.0]SSYLQGTNQITGR
CPTAC-1300: APOB. FVEGSHN[+1.0]STVSLTTK	CPTAC-1301: QPCT. YFQN[+1.0]YSYGGVIQDDHIPFLR	CPTAC-1302: CA1. EIINVGHSFHVNFEDNDN[+1.0]R
CPTAC-1303: VIM. QDVDN[+1.0]ASLAR	CPTAC-1304: DPP7. N[+1.0]LSASVIAVTIQGGAHHLDLR	CPTAC-1305: SERPING1. M[+16.0]LFVEPILEVSSLPTTN[+1.0]STTNSATK
CPTAC-1306: CEACAM8. LFIPN[+1.0]ITTK	CPTAC-1307: DSG2. ESFLAPSSGVQPTLAM[+16.0]PNIAVGQN[+1.0]VTVTER	CPTAC-1308: M6PR. LKPLFN[+1.0]K
CPTAC-1309: ACP2. FNPN[+1.0]ISWQPIPVHTVPITEDR	CPTAC-1310: PCDH1. AN[+1.0]DSDQGANAEIEYTFHQAPEVVR	CPTAC-1311: ITGB8. NYAIIKPIGFN[+1.0]ETAK
CPTAC-1312: CALCOCO2. SAN[+1.0]STLAQALHWTR	CPTAC-1313: MINPP1. N[+1.0]ATALYHVEAFK	CPTAC-1314: KRT40. TYN[+1.0]ASVLPVR
CPTAC-1315: MMP23B. ALM[+16.0]HLN[+1.0]ATLR	CPTAC-1316: CD6. EGDN[+1.0]ITLK	CPTAC-1317: CD6. N[+1.0]ATVVWM[+16.0]K
CPTAC-1318: CD6. TVNSLN[+1.0]VSAISIPEHDEADEISDENR	CPTAC-1319: IRAK2. TILVDN[+1.0]NTWNNTHISR	CPTAC-1320: AEN. LN[+1.0]STAQK
CPTAC-1321: PLTP. N[+1.0]WSLPNR	CPTAC-1322: OVGP1. FVPIYGN[+1.0]HSSVNSVTPQTSPLSLK	CPTAC-2612: MMP23B. ALM[+16.0]HLN[+1.0]ATLR

Chromatograms

Data source: Panorama

	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
y10-98 (2+)	32.6	13	9.8	43.3	16	12.2	54.2	20.6	15.6	15	24	15
y11-98 (2+)	61.6	11.6	9.1	31.4	12.3	9.3	69.1	16.9	13	15	24	15
y11 (2+)	48.9	12.3	8.8	25.9	11.4	10.3	55.3	16.8	13.5	15	24	15
sum	48.8	11.8	8.1	27.7	11.9	9.5	56.1	16.8	12.5	15	24	15

	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+)	8	7.8	6.9	28.3	16	15.6	29.4	17.8	17.1	15	25	15
y7 (1+)	9.2	6.6	6.2	28.7	13.3	14.7	30.1	14.8	16	15	25	15
y6 (1+)	9.4	7.4	6.2	26.7	13	13.6	28.3	15	14.9	15	25	15
sum	8	6.9	6.3	28	14.3	14.8	29.1	15.9	16.1	15	25	15

	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
y10 (1+)	34.2	9.1	5.8	39.2	18.3	15.1	52	20.4	16.2	15	25	15
y9 (1+)	11.7	9.2	5	26	17.8	14.5	28.5	20	15.3	15	25	15
y7 (1+)	18.4	12.9	5	27.5	16.9	14.4	33.1	21.3	15.2	15	25	15
sum	10.6	9.1	4.9	21.5	17.5	14.5	24	19.7	15.3	15	25	15

	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
y9 (2+)	51.5	16.7	20.2	46.4	54.5	38.2	69.3	57	43.2	11	19	13
y11 (2+)	50.3	15.6	22.5	39.7	54.2	37	64.1	56.4	43.3	11	19	13
y5 (1+)	47.1	23.7	42.4	37.2	56.3	53.6	60	61.1	68.3	11	19	13
y9 (1+)	45.2	17.6	18.8	27.3	57.4	36.3	52.8	60	40.9	11	19	13
sum	42.1	15.4	20	30.3	55.7	35.4	51.9	57.8	40.7	11	19	13

	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
y12 (2+)	28.1	6.2	7	15.1	8	9.6	31.9	10.1	11.9	15	24	15
y4 (1+)	27.2	6.4	7.1	23.4	7.3	8.5	35.9	9.7	11.1	15	24	15
y7 (1+)	24.6	8.1	7.7	31.4	11.1	7.8	39.9	13.7	11	15	24	15
y8 (1+)	28.4	6.6	7.7	17.5	8.9	9.6	33.4	11.1	12.3	15	24	15
y9 (1+)	41.2	6.5	3.6	32.6	9.2	10.9	52.5	11.3	11.5	15	24	15
sum	25.8	5.9	6.9	14.1	7.6	8.9	29.4	9.6	11.3	15	24	15

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VIM

Overview Data source: UniProt

Protein Sequence hover to view complete sequence

Protein Map Collapse protein map

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

Assay Details for CPTAC-1018 Collapse assay details

Publication

Assay Parameters Collapse assay parameters

Assay Multiplexing Expand assay panel

Chromatograms

Response Curves

Repeatability

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Assay Details for CPTAC-297 Collapse assay details

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Assay Details for CPTAC-298 Collapse assay details

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Assay Details for CPTAC-1036 Collapse assay details

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Assay Details for CPTAC-1017 Collapse assay details

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Assay Details for CPTAC-1303 Collapse assay details

Assay Parameters Collapse assay parameters

Assay Multiplexing Expand assay panel

Chromatograms

Response Curves

Repeatability

Additional Resources and Comments

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