PXD009740-1

PXD009740 is an original dataset announced via ProteomeXchange.

Title	Peptide Filtering and Quantification Methods
Description	In bottom-up proteomics, data are acquired on peptides resulting from proteolysis. In XIC-based quantification, the quality of the protein abundance estimation depends on how peptide data are filtered and on which quantification method is used to sum up peptide intensities into protein abundances. So far, these two questions have been addressed independently. Here, we studied to which extent the relative performances of the quantification methods depend on the filters applied on peptide intensity data. To this end, we performed a spike-in experiment using Universal Protein Standard (UPS1) to evaluate the performances of five quantification methods, including TOP3, iBAQ, Average of all peptide intensities or log-intensities and intensity modeling, in five datasets obtained after application of four peptide filters based on peptide sharing between proteins, retention time variability, peptides occurrence and peptide intensity profiles. We showed that estimated protein abundances were not equally affected by filters depending on the computation mode (sum or average) and the type of data (intensity or log intensity) used in the quantification methods and that filters could have contrasting effects depending on the quantification objective (absolute or relative). Our results also indicate that intensity modeling was the most robust method, providing the best results in absence of any filter, but that the different quantification methods can reach similar performances when appropriate peptide filters are used. Altogether, our findings provide clues to best handle intensity data according to the quantification objective and to the experimental design.
HostingRepository	PRIDE
AnnounceDate	2018-11-14
AnnouncementXML	Submission_2018-11-14_02:49:25.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mélisande Blein-Nicolas
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	2018-05-10 04:29:12	ID requested
⏵ 1	2018-11-14 02:49:26	announced

Belouah I, Blein-Nicolas M, Balliau T, Gibon Y, Zivy M, Colombi, é S, Peptide filtering differently affects the performances of XIC-based quantification methods. J Proteomics, 193():131-141(2019) [pubmed]

curator keyword: Technical, Biological

submitter keyword: extracted ion current, peptide filtering, quantification methods

Michel Zivy
contact affiliation	Génétique Quantitative et Évolution – Le Moulon PAPPSO INRA – Université Paris-Sud – CNRS – AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France
contact email	michel.zivy@inra.fr
lab head
Mélisande Blein-Nicolas
contact affiliation	Génétique Quantitative et Évolution – Le Moulon INRA – Université Paris-Sud – CNRS – AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France
contact email	melisande.blein-nicolas@inra.fr
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/2018/11/PXD009740

PRIDE project URI

• PRIDE
  1. PXD009740
     1. Label: PRIDE project
     2. Name: Peptide Filtering and Quantification Methods