Introduction
The proteomics field lacks standardized reagents and methods for sample preparation as already adopted in genomic and transcriptomic fields. Current methods are tedious, time-consuming, highly variable, unsuitable for processing large numbers of samples, and tend to negatively affect the robustness of the LC-MS instrumentation. Therefore, we developed an automated sample preparation solution that simplifies and standardizes mass spectrometry (MS) sample preparation. The new automated sample preparation platform is an intuitive turnkey system (instrument, software, reagents) that enables standardized, hands-off operation and provides robust workflows for label-free proteomics and TMT applications.

Methods 
The automated platform enables hands-off protein lysis, DNA removal, protein reduction and alkylation, digestion, TMT labeling, pooling and cleanup, and peptide concentration measurement, providing several workflows and companion reagents to perform several LFQ, TMT11plex, and TMTpro workflows at different sample scales. It guides the researchers across the whole workflow using an embedded user interface to easily place reagents and samples and recover processed samples. A SW ecosystem enables researchers to be assisted during the design of their experiments according to the biological changes. The prepared samples are ready to be injected into the external LC-MS system with known concentrations. The system was used in conjunction with built-for-purpose reagent sets.

Preliminary Date 
The automated sample preparation platform can process up to 36 samples containing 10-100 μg of initial protein input within 4-6 hours depending on the workflows. The final peptides have a minimum missed cleavage rate of less than 5% and complete reduction and alkylation.  Most importantly, the liquid handler has an integrated UV spectrometer that allows peptides to be readily analyzed by LC-MS with a known concentration.