PXD009740 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-05-10 04:29:12 | ID requested | |
⏵ 1 | 2018-11-14 02:49:26 | announced | |
Publication List
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] |
Keyword List
curator keyword: Technical, Biological |
submitter keyword: extracted ion current, peptide filtering, quantification methods |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD009740
- Label: PRIDE project
- Name: Peptide Filtering and Quantification Methods