A systematic evaluation of yeast sample preparation protocols for spectral identifications, proteome coverage and post-isolation modifications

The importance of obtaining comprehensive and accurate information from cellular proteomics experiments asks for a systematic investigation of sample preparation protocols. In particular when working with unicellular organisms with strong cell walls, such as found in the model organism and cell factory Saccharomyces cerevisiae. Here, we performed a systematic comparison of sample preparation protocols using a matrix of different conditions commonly applied in whole cell lysate, bottom-up proteomics experiments. The different protocols were evaluated for their overall fraction of identified spectra, proteome and amino acid sequence coverage, GO-term distribution and number of peptide modifications, by employing a combination of database and unrestricted modification search approaches. Ultimately, the best protocols enabled the identification of approximately 65–70% of all acquired fragmentation spectra, where additional de novo sequencing suggests that unidentified spectra were largely of too low spectral quality to provide confident spectrum matches. Generally, a range of peptide modifications could be linked to solvents, additives as well as filter materials. Most importantly, the use of moderate incubation temperatures and times circumvented excessive formation of modification artefacts. The collected protocols and large sets of mass spectrometric raw data provide a resource to evaluate and design new protocols and guide the analysis of (native) peptide modifications. Significance: The single-celled eukaryote yeast is a widely used model organism for higher eukaryotes in which, for example, the regulation of glycolysis is studied in the context of health and disease. Moreover, yeast is a widely employed cell factory because it is one of the few eukaryotic organisms that can efficiently grow under both aerobic and anaerobic conditions. Large-scale proteomics studies have become increasingly important for single-celled model organisms, such as yeast, in order to provide fundamental understanding of their metabolic processes and proteome dynamics under changing environmental conditions. However, comprehensive and accurate cellular proteomics experiments require optimised sample preparation procedures, in particular when working with unicellular organisms with rigid cell walls, such as found in yeast. Protocols may substantially bias towards specific protein fractions, modify native protein modifications or introduce artificial modifications. That lowers the overall number of spectral identifications and challenges the study of native protein modifications. Therefore, we performed a systematic study of a large array of protocols on yeast grown under highly controlled conditions. The obtained outcomes, the collected protocols and the mass spectrometric raw data enable the selection of suitable sample preparation elements and furthermore support the evaluation of (native) peptide modifications in yeast, and beyond.