Proteomics

Dataset Information

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CHPP chr 1,8,20 proteome dataset using the HCC cell lines of Hep3B and MHCC97H, instrument is AB5600, part 3 of 3


ABSTRACT: The fresh cells as described above were harvested and lysed in buffer containing 8 M Urea, 50 mM NH4HCO3 and 5 mM IAA. The total cell lysates were centrifuged with 12,000 g for 10 min at 4 degrees Celsius to remove cell debris, and 1.5 mg proteins for each cell line were followed by sequential in-solution protein digestion by Lys-C and trypsin at 37 degrees Celsius respectively. The tryptic peptides were cleaned by C18 Sep-Pak column (Waters UK Ltd, Manchester, UK). The mass spectrometer used in this dataset was Triple TOF 5600 (AB SCIEX, Concord, ON). The dataset was produced with two technical replicates and 24 fractions per repeat. The database searching procedure was achieved using Mascot v2.3. The database is Swiss-prot (release 2013 -6).

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver, Permanent Cell Line Cell

SUBMITTER: Zhang Chengpu Zhang Chengpu  

LAB HEAD: Zhang Chengpu Zhang Chengpu

PROVIDER: PXD000535 | Pride | 2013-12-19

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
97H-1-R1.wiff Wiff
97H-1-R1.wiff.scan Wiff
97H-1-R2.wiff Wiff
97H-1-R2.wiff.scan Wiff
97H-10-R1.wiff Wiff
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Publications


We upgraded the preliminary CCPD 1.0 to CCPD 2.0 using the latest deep-profiling proteome (CCPD 2013) of three hepatocellular carcinoma (HCC) cell lines, namely, Hep3B, MHCC97H, and HCCLM3 (ProteomeXchange identifiers: PXD000529, PXD000533, and PXD000535). CCPD 2.0 totally covered 63.6% (438/689) of Chr. 8-coded proteins and 62.6% (439/701) of Chr. 8-coded protein-coding genes. Interestingly, we found that the missing proteins exhibited a tendency to form a cluster region in chromosomes, such as  ...[more]

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