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 AND IMPLEMENTATION: The phosphonormalizer package is freely 
available under GPL ( > =2) license from Bioconductor 
(https://bioconductor.org/packages/phosphonormalizer).
CONTACT: sohrab.saraei@utu.fi or laura.elo@utu.fi.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.