How to process and analyze MS data to quantify and statistically compare protein
abundances in bottom-up proteomics has been an open debate for nearly fifteen years. Two …

Label-free quantitation of proteins analyzed by tandem mass spectrometry uses either
integrated peak intensity from the parent-ion mass analysis (MS1) or features from fragment …

Background Spectral counting methods provide an easy means of identifying proteins with
differing abundances between complex mixtures using shotgun proteomics data. The crux …

Herpesviruses are highly prevalent viruses associated with numerous pathologies both in
animal and human populations. Until now, most of the strategies used to prevent or to cure …

Next‐generation transcriptome sequencing is increasingly integrated with MS to enhance
MS‐based protein and peptide identification. Recently, a breakthrough in transcriptome …

In a previous study, we demonstrated that spectral counts-based label-free proteomic
quantitation could be improved by distributing peptides shared between multiple proteins …

Database searching based methods for label‐free quantification aim to reconstruct the
peptide extracted ion chromatogram based on the identification information, which can limit …

Relative and absolute intensity‐based protein quantification across cell lines, tissue atlases
and tumour datasets is increasingly available in public datasets. These atlases enable …

The Thermo Proteome Discoverer program integrates both peptide identification and
quantification into a single workflow for peptide-centric proteomics. Furthermore, its close …

Measuring the abundance of many proteins over a broad dynamic range requires accurate
quantitation. We show empirically that, in MS experiments, relative quantitation using …