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It is important to investigate the reproducibility of raw mass spectrometry (MS) features of abundance, such as spectral count, peptide number and ion intensity values, when conducting replicate mass spectrometry measurements. Reproducibility can be inferred from these replicate data either formally with analyses of variance techniques or informally with graphical procedures, particularly, Bland-Altman plots on paired runs. In this note, we suggest range plots to provide a suitable generalization of Bland-Altman plots to experiments with more than two replicate runs. We describe range charts and their interpretation, and illustrate their use with data from a recent proteomic study relating to label-free analysis.

Range Charts for Agreement in Measurement Comparison Studies, With Application to Replicate Mass Spectrometry Experiments