Automatic identifification of bacterial species in a polymicrobial sample by MALDI-TOF mass-spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been broadly adopted by routine clinical microbiology laboratories for bacterial species identification.
An isolated colony of the targeted microorganism is the single prerequisite. 
Currently, MS-based microbial identification directly from clinical specimens cannot be routinely performed since it raises two main challenges: 
i) the nature of the sample itself may increase the level of technical variability and bring heterogeneity with respect to the reference database 
and ii) the possibility of encountering polymicrobial samples which will yield a "mixed" MS fingerprint. 
We introduce a new method to infer the composition of polymicrobial samples on the basis of a single mass spectrum.
Our approach relies on a penalized non-negative linear regression framework making use of species-specific prototypes which can be derived directly from the routine reference database of pure spectra.