Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF

ABSTRACT: We present four datasets on proteomics profiling of HeLa and SiHa cell lines associated with the research described in the paper “PROTREC: A probability-based approach for recovering missing proteins based on biological networks”. Proteins in each cell line were acquired by two different data acquisition methods. The first was Data Dependent Acquisition-Parallel Accumulation Serial Fragmentation (DDA-PASEF) and the second was Parallel Accumulation-Serial Fragmentation combined with data-independent acquisition (diaPASEF) . Protein assembly was performed following search against the Swiss-Prot Human database using Peaks Studio for DDA datasets and Spectronaut for DIA datasets . The assembled result contains identified PSMs, peptides and proteins that are above threshold for each HeLa and SiHa sample. Coverage-wise, for DDA-PASEF, approximately 6,090 and 7,298 proteins proteins were quantified for HeLa and SiHA sample, while13,339 and and 8,773 proteins were quantified by diaPASEF for HeLa for SiHa sample respectively.

ORGANISM(S): Homo Sapiens

SUBMITTER: Wilson Wen Bin Goh  

PROVIDER: PXD029773 | iProX | Wed Nov 17 00:00:00 GMT 2021

REPOSITORIES: iProX