Metaproteomics as a Powerful Tool for an Extensive Characterization of Ambient Bioaerosols

Bioaerosols are of great health and environmental concern.
Current
techniques for their characterization are generally designed to detect
individual species or oppositely unspecific molecular tracers. Metaproteomics
on the other hand features the possibility to cover a broad range
of taxonomies in a single analysis. This work presents a successful
application of metaproteomics to characterize the biological fraction
of airborne particulate matter (PM). A bottom-up proteomic strategy
was employed, including protein extraction by ultrasonication in aqueous
buffer, in-solution tryptic digestion, and nanoflow liquid chromatography–high-resolution
mass spectrometry analysis. Extraction parameters were optimized to
enhance proteins’ recovery. The method was validated on Escherichia coli extracts before its application
on ambient PM10 samples collected over 12 weeks in Strasbourg,
France. A total of 1,087 peptides were detected across all samples,
with a weekly average of 223 ± 104 peptides corresponding to
111 ± 40 proteins. Peptides from species belonging to animals,
plants, fungi, bacteria, and archaea kingdoms were inventoried. Many
of them proved to be very relevant, as they were related to human
allergens and pathogens, plant pathogens, or ecological indicators.
In this work, the major benefits of metaproteomics, yet rather unexploited,
as well as its pitfalls and challenges for a broader application in
atmospheric chemistry, are discussed.