SWATH-MS, the next frontier in proteomics

Our basic research team at the Department of Dermatology has recently employed laser-capture microdissection (LCM) coupled with the high sensitive sequential window acquisition of all theoretical mass spectra (SWATH™-MS) proteomics workflow to conduct a comprehensive proteomic profiling of normal skin, actinic keratosis (AK), Bowen’s disease (BD), well differentiated cutaneous squamous cell carcinoma (WD-cSCC), moderately differentiated (MD-)cSCC and poorly differentiated (PD-)cSCC samples. This study follows our previous shotgun proteomic studies of cSCC subtypes.
In our SWATH investigation, we reliably identified and quantified more than 3500 proteins across the samples studied. Our study revealed major proteome changes between the cSCC lesion subtypes which were not previously reported. For the first time, we also showed a strong correlation between the histopathologic variants of cSCC and their corresponding proteome profile. To our knowledge, this is the most comprehensive and complete SWATH™-MS proteomic study in cSCC lesions. The identification of differentially abundant proteins and discriminatory pathways between cSCC lesion subtypes form a rich resource for biomarker discovery and therapeutic targets in the future. Also, the methodology applied in our study will open invaluable opportunities to explore proteome of other skin conditions.
The results of our SWATH study will be presented at the International Society for Mass Spectrometry Conference in Florence, Italy (26-31 August 2018) and at the 27th European Academy of Dermatology and Venerology Congress in Paris, France (12-16 September 2018). Keep an eye on this blog for updates about our proteomic studies of skin lesions.