Fig. 3

Studies in neurodevelopmental disorders using MS-based proteomics. (a) Top-down proteomics allows the identification of protein signatures and specific proteins altered in biological samples, such as blood, urine, and saliva, from affected and unaffected individuals. (b) SILAC and label-based proteomics can be used to combine multiple samples to reduce variability and allow normalization across samples, presenting a powerful tool for time-course based studies in vitro and in vivo. (c) PTM analysis allows the identification of protein modifications that regulate the activity, localization, and stability of the protein. (d) Bottom-up proteomics relies on the digestion of proteins into peptides to allow more precise and accurate quantification and identification through mass spectrometry. It allows for the use of SILAC and label-based proteomics, identification of PTMs, and the ability to identify PINs using proximity-labeling or Co-IP. (e) Co-IP uses antibodies or affinity tags to isolate endogenous proteins and identify strongly interacting proteins that are simultaneously pulled-down, through mass spectrometry. (f) Proximity labeling uses the expression of a protein of interest fused to a labeling-protein, such as BirA* or APEX, which biotinylates proteins in close proximity. These proteins, which include strong and transient interactors, can then be isolated using an avidin pull-down and identified through mass spectrometry. Proximity labeling can allow for the comparison between wildtype, mutant, or condition-treated PINs