QSample: a quality control system to monitor user's samples in proteomics core facilities

Quality in the proteomics laboratory has different facets including instrument performance, sample preparation, tracking of reagents and the establishment of standard operation procedures. We developed some years ago QCloud, a comprehensive automated QC system that supports proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, automated data processing and archiving, and unbiased instrument evaluation.

Following the success on the implementation of QCloud we have now developed QSample, a system that helps to increase the quality and efficiency of the proteomics analyses of user"s samples automatically monitoring the key quality indicators of each sample processed in a proteomics laboratory in almost real time. Specifically, QSample is designed to support proteomics laboratories in the daily quality assessment of different proteomics applications including the analysis of regular proteomes, phospho-proteomes, and protein interactions, using either data-dependent or data-independent acquisition methods. For these workflows, QSample is currently capable of extracting several key quality control parameters that substantially simplify the quality assessment of the proteomics experiments. These parameters include, among others, number of proteins and peptides identified, number of missed cleavages, polymeric contamination and extension of the most common secondary reactions. Furthermore, the system is connected to QCloud to assess the instrument performance during the acquisition of the user"s samples. We have also containerized the QSample code to encapsulate all required dependencies to allow other laboratories to implement it.

In summary, QSample enables for fast evaluation of users" samples, fast-decision making, and therefore, guarantees that proteomics core facilities acquire and deliver data conforming to the best research practice in the scientific community.