Header

UZH-Logo

Maintenance Infos

PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios


Bauer, Chris; Kleinjung, Frank; Rutishauser, Dorothea; Panse, Christian; Chadt, Alexandra; Dreja, Tanja; Al-Hasani, Hadi; Reinert, Knut; Schlapbach, Ralph; Schuchhardt, Johannes (2012). PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios. BMC Bioinformatics, 13:34.

Abstract

BACKGROUND: Recent development of novel technologies paved the way for quantitative proteomics. One of the most important among them is iTRAQ, employing isobaric tags for relative or absolute quantitation. Despite large progress in technology development, still many challenges remain for derivation and interpretation of quantitative results. One of these challenges is the consistent assignment of peptides to proteins. RESULTS: We have developed Peptide Profiling Guided Identification of Proteins (PPINGUIN), a statistical analysis workflow for iTRAQ data addressing the problem of ambiguous peptide quantitations. Motivated by the assumption that peptides uniquely derived from the same protein are correlated, our method employs clustering as a very early step in data processing prior to protein inference. Our method increases experimental reproducibility and decreases variability of quantitations of peptides assigned to the same protein. Giving further support to our method, application to a type 2 diabetes dataset identifies a list of protein candidates that is in very good agreement with previously performed transcriptomics meta analysis. Making use of quantitative properties of signal patterns identified, PPINGUIN can reveal new isoform candidates. CONCLUSIONS: Regarding the increasing importance of quantitative proteomics we think that this method will be useful in practical applications like model fitting or functional enrichment analysis. We recommend to use this method if quantitation is a major objective of research.

Abstract

BACKGROUND: Recent development of novel technologies paved the way for quantitative proteomics. One of the most important among them is iTRAQ, employing isobaric tags for relative or absolute quantitation. Despite large progress in technology development, still many challenges remain for derivation and interpretation of quantitative results. One of these challenges is the consistent assignment of peptides to proteins. RESULTS: We have developed Peptide Profiling Guided Identification of Proteins (PPINGUIN), a statistical analysis workflow for iTRAQ data addressing the problem of ambiguous peptide quantitations. Motivated by the assumption that peptides uniquely derived from the same protein are correlated, our method employs clustering as a very early step in data processing prior to protein inference. Our method increases experimental reproducibility and decreases variability of quantitations of peptides assigned to the same protein. Giving further support to our method, application to a type 2 diabetes dataset identifies a list of protein candidates that is in very good agreement with previously performed transcriptomics meta analysis. Making use of quantitative properties of signal patterns identified, PPINGUIN can reveal new isoform candidates. CONCLUSIONS: Regarding the increasing importance of quantitative proteomics we think that this method will be useful in practical applications like model fitting or functional enrichment analysis. We recommend to use this method if quantitation is a major objective of research.

Statistics

Citations

4 citations in Web of Science®
4 citations in Scopus®
Google Scholar™

Altmetrics

Downloads

64 downloads since deposited on 11 Feb 2013
12 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Language:English
Date:2012
Deposited On:11 Feb 2013 12:57
Last Modified:26 Aug 2017 22:52
Publisher:BioMed Central
ISSN:1471-2105
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1186/1471-2105-13-34
PubMed ID:22340093

Download

Download PDF  'PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios'.
Preview
Content: Published Version
Filetype: PDF
Size: 398kB
View at publisher
Licence: Creative Commons: Attribution 2.0 Generic (CC BY 2.0)