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PXD011725

PXD011725 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleBenchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae
DescriptionComputing absolute protein abundances using mass spectrometry (MS) is a widely used technique in quantitative biology. An important and often overlooked aspect in this methodology is to assess technical reproducibility, i.e. how precise are predictions of abundance when we use the instrument on repeated occasions to measure the same sample. Here, we present a proteomics dataset of Saccharomyces cerevisiae with both biological and inter-run technical triplicates, which we use to analyze both accuracy and precision of the MS instrument. We also investigate how we can improve the quality of predictions by using 4 alternative methods for estimating absolute protein abundance starting from MS intensities. We show that using a simple normalization and rescaling approach performs equally accurate, but much more precise, than methods that rely on external standards. Furthermore, we show that technical reproducibility is significantly lower than biological reproducibility for all the evaluated methods. The results presented here serve as a benchmark for assessing the best way of interpreting MS results to compute protein abundances, and as a consideration of the limitations of the technique when interpreting results.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:01:52.786.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterPetri-Jaan Lahtvee
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-11-19 07:52:52ID requested
12020-04-09 07:10:33announced
22024-10-22 05:01:53announced2024-10-22: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
curator keyword: Biological
submitter keyword: method comparison, quantitative proteomics,yeast
Contact List
Petri-Jaan Lahtvee
contact affiliationInstitute of Technology, University of Tartu, Estonia
contact emaillahtvee@ut.ee
lab head
Petri-Jaan Lahtvee
contact affiliationUniversity of Tartu
contact emaillahtvee@ut.ee
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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