Erik Ahrné

TL;DR: This work uses efficient protein extraction and sample fractionation, as well as state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein-abundance map for Escherichia coli, uncovering system-wide proteome allocation, expression regulation and post-translational adaptations.

TL;DR: It is concluded that a serial Lys-C/trypsin digestion is highly attractive for most applications in quantitative MS-based proteomics building on in-solution digestion schemes.

TL;DR: Five popular low‐cost and easily implemented quantification methods are evaluated and it is shown that only the Top3 method is directly proportional to protein abundance over the full quantification range and is the preferred method in the absence of reference protein measurements.

TL;DR: This analysis defines the molecular diversity of a critical synaptic receptor and provides evidence that neurexin diversity is linked to cellular diversity in the nervous system.

TL;DR: An effective and easy-to-implement remedy that relies on spiking a 6-protein calibration mixture to the samples is proposed and it is found that differentially abundant proteins were assigned dramatically higher statistical significance when quantified using TMT.