Next-generation proteomics relies on high resolution tandem mass spectrometers that allow recording information on thousands of peptides within a few minutes. This huge amount of data opens new horizons in proteomics, especially in the field of proteogenomics and metaproteomics. Proteogenomics aims at characterizing difficult biological models where nucleic acid sequencing should be performed first in order to interpret the proteomic data, and where proteomic data may be useful for better decoding the genomic/transcriptomic information. It is currently applied with success for oncology (oncoproteogenomics) where tumor cells are deriving from the initial reference human genome and for organisms sampled from the environment. Metaproteomics aims at comprehensively identifying the preeminent metabolic pathways for gaining insight into the functions of microbiota. This large scale molecular phenotypic analysis is highly complementary to 16S rRNA metabarcoding and metagenomics. Proteogenomics and metaproteomics have in common to require huge database and informatics capacities. Several examples will be developed to show the potential of both approaches.