Proteomics

Dataset Information

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In-depth proteomic analysis of secretome and whole cells of mouse astrocyte


ABSTRACT: In this study, 3 biological replicates with 3 technical replicates for the conditioned media (CM) and the whole cell lysates (WCL) of C8-D1A cell line were analyzed using 108 LC-MS/MS runs. Each peptide sample was separated into 6 fractions using stageTip based High-pH fractionation. The peptide samples were analyzed using LC-MS/MS instrumentation consisting of a Nanoflow Easy-nLC 1000 that was connected to a Q Exactive mass spectrometer through a nanoelectrospray ion source. All raw files were processed in MaxQuant, version 1.3.0.5 and the Andromeda search engine against the IPI mouse database (version 3.87, 59 534 entries), containing both forward and reverse proteins sequences, and common contaminants. MS/MS searches for the secretome and the whole-cell proteome were performed with the following parameters: carbamidomethylation as a fixed modification; oxidation of methionine and protein N-terminal acetylation as variable modifications; a 20-ppm first-search tolerance; a 6-ppm main-search tolerance. Minimum peptide length was set to six residues. The false discovery rate for all peptides, PTM sites, and protein identifications was set to 0.01.

REANALYSED by: PAe005211

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Dohyun Han  

LAB HEAD: Dohyun Han

PROVIDER: PXD000501 | Pride | 2014-06-05

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
20130521_C8D1A_whole_set1_F1_1.raw Raw
20130521_C8D1A_whole_set1_F1_2.raw Raw
20130521_C8D1A_whole_set1_F1_3.raw Raw
20130521_C8D1A_whole_set1_F2_1.raw Raw
20130521_C8D1A_whole_set1_F2_2.raw Raw
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Publications

Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation.

Han Dohyun D   Jin Jonghwa J   Woo Jongmin J   Min Hophil H   Kim Youngsoo Y  

Proteomics 20140528 13-14


Astrocytes are the most abundant cells in the CNS, but their function remains largely unknown. Characterization of the whole-cell proteome and secretome in astrocytes would facilitate the study of their functions in various neurodegenerative diseases and astrocyte-neuron communication. To build a reference proteome, we established a C8-D1A astrocyte proteome to a depth of 7265 unique protein groups using a novel strategy that combined two-step digestion, filter-aided sample preparation, StageTip  ...[more]

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