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PXD028901-2

PXD028901 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMSLibrarian: Optimized predicted spectral libraries for DIA proteomics
DescriptionData-independent mass spectrometry is the method of choice for deep, consistent and accurate single-shot profiling in bottom-up proteomics. While classic workflows required auxiliary DDA-MS analysis of subject samples to derive prior knowledge spectral libraries for targeted quantification from DIA-MS maps, library-free approaches based on in silico predicted libraries promise deep DIA-MS profiling with reduced experimental effort and cost. Coverage and sensitivity in such analyses, however, is limited, in part, by large library size and persistent deviations from experimental data. We present MSLibrarian, a workflow and tool to obtain optimized predicted spectral libraries by the integrated usage of spectrum-centric DIA data interpretation via the DIA-Umpire approach to inform and calibrate the in silico predicted library approach. Predicted-vs-observed comparisons enable optimization of intensity prediction parameters, calibration of retention time prediction for deviating chromatographic setups and optimization of library scope and sample representativeness. Benchmarking via a dedicated ground-truth-embedded species mixture experiment and quantitative ratio-validation confirms gains of up to 9 % on precursor and 7 % protein level at equivalent FDR control and validation criteria. MSLibrarian has been implemented as open-source R software package and, with step-by-step usage instructions, is availabe at https://github.com/MarcIsak/MSLibrarian.
HostingRepositoryPRIDE
AnnounceDate2022-01-17
AnnouncementXMLSubmission_2022-01-18_01:46:30.265.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChristofer Karlsson
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListcarbamoylated residue
InstrumentQ Exactive HF-X
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-10-04 04:44:35ID requested
12022-01-17 09:19:45announced
22022-01-18 01:46:30announced2022-01-18: Updated publication reference for DOI(s): 10.1021/acs.jproteome.1c00796.
32023-11-14 08:53:43announced2023-11-14: Updated project metadata.
Publication List
10.1021/acs.jproteome.1c00796;
Keyword List
submitter keyword: DIA, predicted spectral library, Q-Exactive, HF-X, LFQ bench
Contact List
Johan Malmström
contact affiliationInfection Medicine Proteomics Lab, Division of Infection Medicine (BMC), Faculty of Medicine, Lund University, Lund, Sweden
contact emailjohan.malmstrom@med.lu.se
lab head
Christofer Karlsson
contact affiliationLund University
contact emailChristofer.Karlsson@med.lu.se
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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