Quantitative assessment of strain isolates and microbiomes using fast MS/MS-free metaproteomics

Microbial proteomics and metaproteomic studies rely heavily on mass spectrometry. Standard liquid chromatography/tandem mass spectrometry-based methods for protein identification and quantitation exhibit lengthy analysis time. Here, we report on the implementation of the previously developed DirectMS1 approach for metaproteomics studies that provides a unique combination of accurate protein quantitation and rapid analysis time. We validated our method using a series of proteome-wide analyses of bacterial samples including strain isolates, mock microbiomes composed of bacteria spiked at known concentrations and human fecal microbiomes. We demonstrated that the developed two-stage search algorithm identifies the bacterial isolate species with an accuracy of 95%, when no prior information on the sample is available. Microbiome composition was resolved at the genus level with the mean difference between the actual and identified microbiome components of 12%. Pearson coefficient of up to 0.97 was achieved in estimates of strain biomass change in mock microbiome samples. By the example of Rhodococcus biodegradation of n-alkanes, phenols and its derivatives, we showed that our approach effectively characterizes changes in the activity of metabolic pathways of strain isolates. For the benchmarking, the changes in biodegradation activity were also assessed using the standard label-free and TMT DDA approaches.