Assessment of ultrasonic-assisted enzymatic digestion of complex protein mixtures by high-resolution mass

Background & Objectives Large-scale proteome analysis by mass spectrometry is commonly preceded by enzymatic digestion of proteins. The conventional protocol for in-solution digest of complex protein mixtures includes trypsin and is performed at room temperature for at least 12h. To improve this time-consuming method we assessed the efficiency of focused ultrasoundassisted enzymatic digest. It has previously been shown that ultrasonication can dramatically reduce digestion time. However, it is not known how this affects protein identification and quantification when applied to complex protein mixtures such as whole cell lysates. Here, we explore in-depth the proteome of embryonic stem cells comparing trypsindigestion methods with and without ultrasound support side-by-side. Methods