A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä
Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics
Tekijät: Sohrab Saraei, Tomi Suomi, Otto Kauko, Laura L. Elo
Kustantaja: Oxford University Press
Kustannuspaikka: Oxford
Julkaisuvuosi: 2018
Journal: Bioinformatics
Artikkelin numero: btx573
Vuosikerta: 34
Numero: 4
Aloitussivu: 693
Lopetussivu: 694
Sivujen määrä: 2
ISSN: 1367-4803
eISSN: 1460-2059
DOI: https://doi.org/10.1093/bioinformatics/btx573(external)
Rinnakkaistallenteen osoite: https://research.utu.fi/converis/portal/detail/Publication/28544998(external)
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.
Ladattava julkaisu This is an electronic reprint of the original article. |  |
