HDAC1, CPTAC-2607 - 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
HDAC1	RPD3L1

Sequence Length (AA)	Molecular Weight (Da)
482	55103

Protein Name
Histone deacetylase 1

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MAQTQGTRRK	VCYYYDGDVG	NYYYGQGHPM	KPHRIRMTHN	LLLNYGLYRK
60	70	80	90	100
MEIYRPHKAN	AEEMTKYHSD	DYIKFLRSIR	PDNMSEYSKQ	MQRFNVGEDC
110	120	130	140	150
PVFDGLFEFC	QLSTGGSVAS	AVKLNKQQTD	IAVNWAGGLH	HAKKSEASGF
160	170	180	190	200
CYVNDIVLAI	LELLKYHQRV	LYIDIDIHHG	DGVEEAFYTT	DRVMTVSFHK
210	220	230	240	250
YGEYFPGTGD	LRDIGAGKGK	YYAVNYPLRD	GIDDESYEAI	FKPVMSKVME
260	270	280	290	300
MFQPSAVVLQ	CGSDSLSGDR	LGCFNLTIKG	HAKCVEFVKS	FNLPMLMLGG
310	320	330	340	350
GGYTIRNVAR	CWTYETAVAL	DTEIPNELPY	NDYFEYFGPD	FKLHISPSNM
360	370	380	390	400
TNQNTNEYLE	KIKQRLFENL	RMLPHAPGVQ	MQAIPEDAIP	EESGDEDEDD
410	420	430	440	450
PDKRISICSS	DKRIACEEEF	SDSEEEGEGG	RKNSSNFKKA	KRVKTEDEKE
460	470	480	482
KDPEEKKEVT	EEEKTKEEKP	EAKGVKEEVK	LA

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-2607 Collapse assay details

Data source: Panorama

Official Gene Symbol: HDAC1
Peptide Sequence: YGEYFPGTGDLR
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 201
Peptide End: 212

CPTAC ID: CPTAC-2607
Peptide Molecular Mass: 1,373.6252
Species: Homo sapiens (Human)
Assay Type: Direct MRM
Matrix: Human ovarian tumor tissue digest
Submitting Laboratory: Johns Hopkins University
Submitting Lab PI: Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument: TSQ Vantage
Internal Standard: Stable isotope-labeled peptides
Peptide Standard Purity: Crude (~60%)
Peptide Standard Label Type: 13C and 15N at C-terminus R

LC: Accela 1250 Quaternary Low Pump
Column Packing: C18, 3 µm, 300 Å
Column Dimensions: 1.0 mm I.D. x 15 cm
Flow Rate: 50 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-I

CPTAC-2597: ACE. ELYEPIWQN[+1.0]FTDPQLR	CPTAC-2598: BST1. N[+1.0]C[+57.0]TAIWEAFK	CPTAC-2599: HYOU1. VIN[+1.0]ETWAWK
CPTAC-2600: ICOSLG. TDNSLLDQALQN[+1.0]DTVFLNM[+16.0]R	CPTAC-2601: IGF2R. TN[+1.0]ITLVC[+57.0]KPGDLESAPVLR	CPTAC-2602: PECAM1. DDVLFYN[+1.0]ISSM[+16.0]K
CPTAC-2603: PLXNB2. SIN[+1.0]VTGQGFSLIQR	CPTAC-2604: TNC. LLETVEYN[+1.0]ISGAER	CPTAC-2605: KAT5. SHDDIVTR
CPTAC-2606: KAT5. GFHIVGYFSK	CPTAC-2607: HDAC1. YGEYFPGTGDLR	CPTAC-2608: TP53BP1. ITDVYYVDGTEVER
CPTAC-2609: TP53BP1. WSSNGYFYSGK	CPTAC-2610: BRCA1. TSVYIELGSDSSEDTVNK	CPTAC-2611: BRCA1. SVESNIEDK

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
y9 (1+)	13.8	3.9	6.8	11.1	6.5	7.5	17.7	7.6	10.1	15	15	15
y8 (1+)	14.3	6.7	5.9	12.6	9.4	6.4	19.1	11.5	8.7	15	15	15
y7 (1+)	4.9	4.2	4.5	6.2	7.2	5.3	7.9	8.3	7	15	15	15
sum	5.3	4.2	4.5	5.9	7.2	5.3	7.9	8.3	7	15	15	15

Additional Resources and Comments

Resources

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View Peptide in Panorama

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Comments

Assay Details for CPTAC-1248 Collapse assay details

Data source: Panorama

Official Gene Symbol: HDAC1
Peptide Sequence: YYAVNYPLR
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 221
Peptide End: 229

CPTAC ID: CPTAC-1248
Peptide Molecular Mass: 1,157.5869
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