A1 Refereed original research article in a scientific journal

Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics



Authors: Sohrab Saraei, Tomi Suomi, Otto Kauko, Laura L. Elo

Publisher: Oxford University Press

Publishing place: Oxford

Publication year: 2018

Journal: Bioinformatics

Article number: btx573

Volume: 34

Issue: 4

First page : 693

Last page: 694

Number of pages: 2

ISSN: 1367-4803

eISSN: 1460-2059

DOI: https://doi.org/10.1093/bioinformatics/btx573

Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/28544998


Abstract
MOTIVATION: Global centering-based normalization is a commonly-used normalization approach in mass spectrometry-based label-free proteomics. It scales the peptide abundances to have the same median intensities, based on an assumption that the majority of abundances remain the same across the samples. However, especially in phosphoproteomics, this assumption can introduce bias, as the samples are enriched during sample preparation which can mask the underlying biological changes. To address this possible bias, phosphopeptides quantified in both enriched and non-enriched samples can be used to calculate factors that mitigate the bias.

RESULTS: We present an R package phosphonormalizer for normalizing enriched samples in label-free mass spectrometry-based phosphoproteomics.

AVAILABILITY: The phosphonormalizer package is freely-available under GPL ( > =2) license from Bioconductor ( https://bioconductor.org/packages/phosphonormalizer ).

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Last updated on 2024-26-11 at 12:49