Indeed, protein and DNA sequencing data can be used alongside one another to yield more robust evidence. At the American Society for Mass Spectrometry (ASMS 2019), our group reported data showing protein sequencing can be just as accurate as DNA sequencing and can fill in DNA sequencing gaps . However, protein sequencing, and specifically de novo protein sequencing, has yet to be routinely used for proteome discovery. The most often used approach is protein identification by mass spectrometry that relies on homology searching and comparison using databases built from DNA sequencing information. However, they still offer a glimpse of protein sequencing’s great potential.
Most recently, a News Feature in Nature showcased the importance of MS-based protein identification of ancient human remains . Through the passage of time, DNA may degrade, endure damage (resulting in missing segments), and become scarce. Reconstitution of the entire target genome through DNA sequencing then becomes a painstaking, near impossible task. This is the reason why samples must be as fresh as possible for DNA sequencing. However, proteins are often more stable and stick around longer than DNA. Proteins often remain in teeth and bone, and even if some degradation has occurred, the protein’s building blocks – peptides, will still be available to perform MS-based identification .
Such was the case in the study by Chen et al. published in Nature in May of this year . This is the first study to identify ancient hominin with proteins, which marks an exciting milestone in proteomics. In their paper, they utilized already reported DNA data from other hominin and their own MS-based analysis of peptides of an ancient hominin found in the Tibetan Plateau in Baishiya Karst Cave, Xiahe, Gansu, China. Thanks to MS-based analysis, they could conclude that the fossils belonged to a Denisovan, providing evidence that Denisovans likely resided in a larger geographical area than previously thought – well outside the Altai Mountains, where the infamous Siberian Denisova Cave lies . This study sets a precedent that protein sequencing could be used in the analysis of organisms’ fossils where DNA is unavailable or scant.