Site‐specific analysis of bacterial phosphoproteomes

Protein phosphorylation on serine, threonine and tyrosine is established as an important regulatory modification in bacteria. A growing number of studies employing mass spectrometry‐based proteomics report large protein phosphorylation datasets, providing precise evidence for in‐vivo phosphorylation that is especially suitable for functional follow‐up. Here, we provide an overview of the strategies currently used in bacterial phosphoproteomics, with an emphasis on gel‐free proteomics and approaches that enable global detection of phosphorylation sites in bacterial proteins. The proteomics technology has matured sufficiently to permit routine characterization of phosphoproteomes and phosphopeptides with high sensitivity; we argue that the next challenge in the field will be the large‐scale detection of protein kinase and phosphatase substrates and their integration into regulatory networks of the bacterial cell.