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PXD034709

PXD034709 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleBenchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics
DescriptionThis 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.
HostingRepositoryiProX
AnnounceDate2022-12-08
AnnouncementXMLSubmission_2023-01-12_19:43:58.996.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterShanshan Li
SpeciesList scientific name: Mus musculus; NCBI TaxID: 10090; scientific name: Saccharomyces cerevisiae S288C; NCBI TaxID: 559292; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListphosphorylated residue
InstrumentQ Exactive HF; Q Exactive HF-X; timsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-06-20 01:25:26ID requested
12022-12-08 18:22:54announced
22023-01-12 19:43:59announced2023-01-13: 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 affiliationShanghaiTech University
contact emailshuiwq@shanghaitech.edu.cn
lab head
Shanshan Li
contact affiliationShanghaiTech University
contact emaillishsh@shanghaitech.edu.cn
dataset submitter
Full Dataset Link List
iProX dataset URI