PXD011725-2

PXD011725 is an original dataset announced via ProteomeXchange.

Title	Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae
Description	Computing 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:01:52.786.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Petri-Jaan Lahtvee
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-19 07:52:52	ID requested
1	2020-04-09 07:10:33	announced
⏵ 2	2024-10-22 05:01:53	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: method comparison, quantitative proteomics,yeast

Petri-Jaan Lahtvee
contact affiliation	Institute of Technology, University of Tartu, Estonia
contact email	lahtvee@ut.ee
lab head
Petri-Jaan Lahtvee
contact affiliation	University of Tartu
contact email	lahtvee@ut.ee
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/04/PXD011725

PRIDE project URI

• PRIDE
  1. PXD011725
     1. Label: PRIDE project
     2. Name: Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae