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Background  Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM) analysis like reversible cysteine oxidation are evaluated. The paper proposes a pipeline based on the R programming language to analyze PTMs from peptide-centric label-free quantitative proteomics data.    Results  Our methodology includes variance stabilization, normalization, and missing data imputation to account for the large dynamic range of PTM measurements. It also corrects biases from an enrichment protocol and reduces the random and systematic errors associated with label-free quantification. The performance of the methodology is tested by performing proteome-wide differential PTM quantitation using linear models analysis ( limma ). We objectively compare two imputation methods along with significance testing when using multiple-imputation for missing data.    Conclusion  Identifying PTMs in large-scale datasets is a problem with distinct characteristics that require new methods for handling missing data imputation and differential proteome analysis. Linear models in combination with multiple-imputation could significantly outperform a  t -test-based decision method.    Electronic supplementary material  The online version of this article (10.1186/s12859-019-2619-6) contains supplementary material, which is available to authorized users.

Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics