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DDA-PASEF and diaPASEF acquired A549/K562 proteomic datasets with deliberate batch effects

ABSTRACT: We generated two comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent and Data-Indepentdent Acquisition modes. This dataset contain a balanced two-class design (cell lines: A549 vs K562), allowing for investigating mixed effects from class, batch and acquisition method. Investigators can also compare and integrate DDA and DIA platforms, delve into the various patterns and mechanisms of missing values, benchmark batch effects correction algorithms and assess confounding between different technical issues.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: HE WANG

LAB HEAD: Wilson Goh

PROVIDER: PXD041421 | Pride | 2023-11-21

REPOSITORIES: Pride

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MultiPro: DDA-PASEF and diaPASEF acquired cell line proteomic datasets with deliberate batch effects.

Wang He H Lim Kai Peng KP Kong Weijia W Gao Huanhuan H Wong Bertrand Jern Han BJH Phua Ser Xian SX Guo Tiannan T Goh Wilson Wen Bin WWB

Scientific data 20231202 1

Mass spectrometry-based proteomics plays a critical role in current biological and clinical research. Technical issues like data integration, missing value imputation, batch effect correction and the exploration of inter-connections amongst these technical issues, can produce errors but are not well studied. Although proteomic technologies have improved significantly in recent years, this alone cannot resolve these issues. What is needed are better algorithms and data processing knowledge. But t ...[more]

PMID: 38042886

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