PXD034709-2
PXD034709 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics |
| Description | This repository is related to the work "Benchmarking commonly usedsoftware suites and analysis workflows for DIA proteomics and phosphoproteomics". The following files are stored here: 1. four MS datasets generated in this work, including two two-species benchmark datasets acquired on QE HF and timsTOF Pro, and two TNF-alpha induced phosphoproteomics datasets acquired on QE HF-X and timsTOF Pro; 2. all spectral libraries used in this work; 3. raw MS data search reports with analysis logs included if software reported; 4. preprocessed MS data search reports for any result from HF and TIMS DIA benchmark datasets; 5. FASTAs used in this work; 6. a description file (Description_of_iProX_and_public_data.xlsx) for the stored files in this repository and other public data used in this work. Note: 3 and 4 are packed into one zip file for each data search experiment. |
| HostingRepository | iProX |
| AnnounceDate | 2022-12-08 |
| AnnouncementXML | Submission_2023-01-12_19:43:58.996.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Shanshan Li |
| SpeciesList | scientific name: Mus musculus; NCBI TaxID: 10090; scientific name: Saccharomyces cerevisiae S288C; NCBI TaxID: 559292; scientific name: Homo sapiens; NCBI TaxID: 9606; |
| ModificationList | phosphorylated residue |
| Instrument | Q Exactive HF; Q Exactive HF-X; timsTOF Pro |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2022-06-20 01:25:26 | ID requested | |
| 1 | 2022-12-08 18:22:54 | announced | |
| ⏵ 2 | 2023-01-12 19:43:59 | announced | 2023-01-13: Update publication information. |
Publication List
| Lou R, Cao Y, Li S, Lang X, Li Y, Zhang Y, Shui W, Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics. Nat Commun, 14(1):94(2023) [pubmed] |
Keyword List
| submitter keyword: DIA, Benchmarking, global proteomics, phosphoproteomics |
Contact List
| Wenqing Shui | |
|---|---|
| contact affiliation | ShanghaiTech University |
| contact email | shuiwq@shanghaitech.edu.cn |
| lab head | |
| Shanshan Li | |
| contact affiliation | ShanghaiTech University |
| contact email | lishsh@shanghaitech.edu.cn |
| dataset submitter | |
Full Dataset Link List
| iProX dataset URI |
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