The remarkable flexibility and adaptability of ensemble methods and deep learning models
have led to the proliferation of their application in bioinformatics research. Traditionally …

Proteins are major building blocks of life. The protein content of a cell and an organism
provides key information for the understanding of biological processes and disease. Despite …

From a molecular perspective, enactors of function in biology are intact proteins that can be
variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 …

Protein digestion using a dedicated protease represents a key element in a typical mass
spectrometry (MS)-based shotgun proteomics experiment. Up to now, digestion has been …

Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to
identify and quantify the peptides generated by the proteolysis of a biological sample …

The proteome is a dynamic system in which each protein has interconnected properties—
dimensions—that together contribute to the phenotype of a cell. Measuring these properties …

We describe the comprehensive analysis of the yeast proteome in just over one hour of
optimized analysis. We achieve this expedited proteome characterization with improved …

Mass spectrometry-based proteomics has greatly benefitted from enormous advances in
high resolution instrumentation in recent years. In particular, the combination of a linear ion …

Protein structural changes induced by external perturbations or internal cues can profoundly
influence protein activity and thus modulate cellular physiology. A number of biophysical …

Systems biology requires comprehensive data at all molecular levels. Mass spectrometry
(MS)-based proteomics has emerged as a powerful and universal method for the global …