Proteomic 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 ac...
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Elsevier
2022-04-01
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| Series: | Data in Brief |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340922001317 |
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| author | Zelu Huang Weijia Kong Bertrand Jernhan Wong Huanhuan Gao Tiannan Guo Xianming Liu Xiaoxian Du Limsoon Wong Wilson Wen Bin Goh |
| author_facet | Zelu Huang Weijia Kong Bertrand Jernhan Wong Huanhuan Gao Tiannan Guo Xianming Liu Xiaoxian Du Limsoon Wong Wilson Wen Bin Goh |
| author_sort | Zelu Huang |
| collection | DOAJ |
| description | 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 HeLa and SiHa sample. Coverage-wise, for DDA-PASEF, approximately 6,090 and 7,298 proteins were quantified for HeLa and SiHA sample, while13,339 and 8,773 proteins were quantified by diaPASEF for HeLa for SiHa sample, respectively. Consistency-wise, diaPASEF has fewer missing values (∼ 2%) compared to its DDA counterparts (∼5–7%). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository [4] with the dataset identifier PXD029773. |
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| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-12-13T09:02:02Z |
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| series | Data in Brief |
| spelling | doaj.art-a6d81644122d41489e1ef14c99b9ba162022-12-21T23:53:09ZengElsevierData in Brief2352-34092022-04-0141107919Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEFZelu Huang0Weijia Kong1Bertrand Jernhan Wong2Huanhuan Gao3Tiannan Guo4Xianming Liu5Xiaoxian Du6Limsoon Wong7Wilson Wen Bin Goh8School of Chemical and Biomedical Engineering, Nanyang Technological University, SingaporeSchool of Biological Sciences, Nanyang Technological University, Singapore; Department of Computer Science, National University of Singapore, SingaporeSchool of Biological Sciences, Nanyang Technological University, SingaporeZhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Zhejiang, ChinaZhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Zhejiang, ChinaBruker (Beijing) Scientific Technology Co., Ltd, Shanghai, ChinaBruker (Beijing) Scientific Technology Co., Ltd, Shanghai, ChinaDepartment of Computer Science, National University of Singapore, Singapore; Corresponding author at: School of Biological Sciences and Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.School of Biological Sciences, Nanyang Technological University, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Corresponding author at: School of Biological Sciences, Nanyang Technological University, Singapore.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 HeLa and SiHa sample. Coverage-wise, for DDA-PASEF, approximately 6,090 and 7,298 proteins were quantified for HeLa and SiHA sample, while13,339 and 8,773 proteins were quantified by diaPASEF for HeLa for SiHa sample, respectively. Consistency-wise, diaPASEF has fewer missing values (∼ 2%) compared to its DDA counterparts (∼5–7%). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository [4] with the dataset identifier PXD029773.http://www.sciencedirect.com/science/article/pii/S2352340922001317DDADIAPASEFHeLaSiHa |
| spellingShingle | Zelu Huang Weijia Kong Bertrand Jernhan Wong Huanhuan Gao Tiannan Guo Xianming Liu Xiaoxian Du Limsoon Wong Wilson Wen Bin Goh Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF Data in Brief DDA DIA PASEF HeLa SiHa |
| title | Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF |
| title_full | Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF |
| title_fullStr | Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF |
| title_full_unstemmed | Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF |
| title_short | Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF |
| title_sort | proteomic datasets of hela and siha cell lines acquired by dda pasef and diapasef |
| topic | DDA DIA PASEF HeLa SiHa |
| url | http://www.sciencedirect.com/science/article/pii/S2352340922001317 |
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