Dataset Information

A comprehensive CHO SWATH-MS spectral library for accurate quantitative profiling of 10k proteins

ABSTRACT: A comprehensive Chinese hamster ovary (CHO)-cell specific spectral library, containing extensive information of high-quality spectral ions covering more than 10k CHO cell proteins, was constructed to provide confident and reproducible protein identification and quantification in data-independent SWATH-MS analysis. The applicability of CHO spectral library was tested in the analyses of different CHO samples including whole cell lysate, harvested cell culture fluids, and downstream processing samples. The portability of CHO spectral library was also demonstrated in the processing and analyses of SWATH-MS data sets collected from multiple LC-MS instrumental setups and various CHO cell lines.

INSTRUMENT(S): TripleTOF 5600+, TripleTOF 6600

ORGANISM(S): Cricetulus Griseus (chinese Hamster) (cricetulus Barabensis Griseus)

TISSUE(S): Epithelial Cell

SUBMITTER: Kae Hwan Sim

LAB HEAD: Xuezhi Bi

PROVIDER: PXD016047 | Pride | 2020-07-20

REPOSITORIES: Pride

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A comprehensive CHO SWATH-MS spectral library for robust quantitative profiling of 10,000 proteins.

Sim Kae Hwan KH Liu Lillian Chia-Yi LC Tan Hwee Tong HT Tan Kelly K Ng Daniel D Zhang Wei W Yang Yuansheng Y Tate Stephen S Bi Xuezhi X

Scientific data 20200811 1

Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) is a data-independent acquisition (DIA) strategy that requires a specific spectral library to generate unbiased and consistent quantitative data matrices of all peptides. SWATH-MS is a promising approach for in-depth proteomic profiling of Chinese hamster Ovary (CHO) cell lines, improving mechanistic understanding of process optimization, and real-time monitoring of process parameters in biologics R&D and manufacturing ...[more]

PMID: 32782267

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Project description:Î³-secretase is an intra-membrane-cleaving aspartyl protease implicated in the processing of a wide range of type I membrane proteins including the Notch receptor and the amyloid-Î² precursor protein (APP). It thus regulates a diverse array of cellular and biological processes including the differentiation of neuronal embryonic stem cells, or intestinal stem cells, with the latter controlling the self-renewing of the intestinal epithelium. Indeed, proteolysis of these proteins by Î³-secretase triggers signaling cascades by releasing intracellular domains (ICDs) which, following association with adaptor proteins and nuclear translocation, modulate the transcription of different genes by binding directly to their promoters. The pronounced proliferative and regenerative effects of Notch signaling and its implication in the generation of the AÎ²-peptides, makes Î³-secretase a therapeutic target for several types of cancer and for Alzheimerâs disease. To investigate the broad effects of Î³-secretase activity onto the cellular transcriptome, Chinese hamster ovary (CHO) cells with enhanced Î³-secretase were compared to cells with abolished Î³-secretase activity via a microarray designed for a genetically close species, mouse. Our findings will potentially help to decipher the biology of Î³-secretase, including a better understanding of the roles of this enzyme in gene transcription. We compared the transcriptomes of two CHO cell lines displaying extreme differences in Î³-secretase activity. The S-1 cell line overexpressed the four components of Î³-secretase (NCT, APH1aL, PS1, and PEN2) and was characterized by a marked increase in the level of PS1 heterodimers associated with 8-fold increased Î³-secretase activity compared to untransfected controls. The other cell line consisted of wild type CHO cells incubated with DAPT, a well-known Î³-secretase inhibitor. The two cell lines were used in combination with a mouse microarray to analyze gene transcription under enhanced Î³-secretase. Two samples, S1 and DAPT treated CHO- were used in biological triplicates each.

Dataset Information

A comprehensive CHO SWATH-MS spectral library for accurate quantitative profiling of 10k proteins

Publications

A comprehensive CHO SWATH-MS spectral library for robust quantitative profiling of 10,000 proteins.

Similar Datasets

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