Semi-supervised quality control method for proteome analyses based on tandem mass spectrometry

Abstract

With the increasing volume of bottom-up proteome analyses using liquid chromatography/mass spectrometry (LC–MS), a rapid and easy for interpretation assessment of the experimental system performance becomes an essential part of the analytical workflow. A variety of the so-called quality control (QC) tools measuring this performance in advance of sophisticated and expensive analyses have been developed and used in practice in many proteomic laboratories worldwide. In the attempts of covering all aspects of LC–MS instrument operation, these tools are typically loaded with a high number of metrics that require performing large-scale analyses using complex standard digest mixtures followed by extensive data processing. Yet, a rapid and simple assessment of the instrument’s readiness for a large-scale proteome analysis is often everything needed in routine laboratory practice. In this work we propose a new MS/MS-based quality score which allows performing this assessment without employing full-scale experimental work with annotated samples and time-consuming data analysis. The proposed metric shows high specificity and accurate assessment of the analytical runs and can be used with single protein digest standards. It also allows clear graphical visualization of the quality of the run that makes it useful for day-to-day practice.