biostudies-literatureHuang ZMinistry of Education - Singapore107919https://www.ebi.ac.uk/biostudies/studies/S-EPMC8844217biostudies-literatureUnknown41We 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" [1]. 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) [2], [3]. 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 Data in briefProteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF.PMC8844217RG35/20Liu XWong BJHuang ZWong LDu XGuo TGao HKong WGoh WWBfalseProteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF.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" [1]. 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) [2], [3]. 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 2022-01-01T00:00:00Z2022 Apr2025-04-21T17:06:10.182Z2025-04-21T17:06:10.182ZS-EPMC88442173519869110.1016/j.dib.2022.107919