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 Q Exactive, part 2 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 Q-Exactive. 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): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver, Permanent Cell Line Cell

SUBMITTER: Zhang Chengpu Zhang Chengpu  

LAB HEAD: Zhang Chengpu Zhang Chengpu

PROVIDER: PXD000533 | Pride | 2013-12-16

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
3B1-1.raw Raw
3B1-2.raw Raw
3B10-1.raw Raw
3B10-2.raw Raw
3B11-1.raw Raw
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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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