Using ProteomicsDB to analyze the human proteome
ProteomicsDB is a new resource that is likely underutilized due to the technical expertise required to use an API. This mass-spec database contains a wealth of information, including different kinds of protein modifications. I know how to use the API, but I am not an expert at mass-spec data or protein modifications and do not intend on publishing on these topics. With that said, I do think it would be interesting to check how many of the modifications present in this database are already known or have been predicted, and if this data can be used to validate predicted protein modifications. If there are a high number of novel protein modifications, could these be used to identify novel motifs, for example kinase motifs? This code will download data from ProteomicsDB in xml format, parse it for the modification of interest, and collect the results in a user friendly manner. For information on how to use the code watch the video below.
