Post-Translational Modification (PTM) Proteomics: Challenges and Perspectives

Bayesian false discovery rates for post-translational modification proteomics

Tandem mass spectrometry-based proteomics enables high throughput analysis of post-translational modifications (PTMs) on proteins. In current researches of shotgun proteomics, peptides with various PTMs and those without PTMs are often identified together and an overall false discovery rate (FDR) is estimated. However, it is often the case that only a subset of identifications, e.g. those with ...

SILAC-based Quantitative Post Translational Modification (PTM) Profile Analysis with PEAKS

Allosteric post-translational modification codes.

Post-translational modifications (PTMs) have been recognized to impact protein function in two ways: (i) orthosterically, via direct recognition by protein domains or through interference with binding; and (ii) allosterically, via conformational changes induced at the functional sites. Because different chemical types of PTMs elicit different structural alterations, the effects of combinatorial...

Post-translational modification by SUMO.

Post-translational modifications (PTMs) are chemical alterations to a protein following translation, regulating stability and function. Reversible phosphorylation is an example of an important and well studied PTM involved in a number of cellular processes. SUMOylation is another PTM known to modify a large number of proteins and plays a role in various cellular processes including: cell cycle ...

Global Post-Translational Modification Discovery

A new global post-translational modification (PTM) discovery strategy, G-PTM-D, is described. A proteomics database containing UniProt-curated PTM information is supplemented with potential new modification types and sites discovered from a first-round search of mass spectrometry data with ultrawide precursor mass tolerance. A second-round search employing the supplemented database conducted wi...