EMERGE Episode 14: Using an Orbitrap for Phosphoproteomics, Exploring the Effect of Parameters скачать в хорошем качестве

EMERGE Episode 14: Using an Orbitrap for Phosphoproteomics, Exploring the Effect of Parameters

Phosphoproteomics is a biologically important and dynamic field, with researchers constantly seeking new ways to improve phosphopeptide detection, quantity and quality. Data-dependent mass spectrometry (DDA-MS) is the current gold standard for phosphoproteomics and high-throughput sample preparation is quickly becoming the norm, allowing researchers from diverse research fields access to instrumentation and data. With so many researchers not necessarily familiar with DDA-MS, the instrument parameters can lead to sub-optimal results, particularly for the detection of phosphopeptides. To demonstrate the principle, the response of phosphopeptide quantity and quality is analyzed with changing parameters on an Orbitrap, leading to optimization for un-enriched samples to phospho-enriched samples, illustrating how optimization of phosphopeptide detection is not necessarily a binary outcome. These investigations provide a roadmap for those unfamiliar with many of the commonly-used parameters in DDA-MS, an explanation for selecting certain values over others, and some insight into their effects on phosphopeptide analysis.