Have you ever digested a single "purified" human protein from a commercial source and compared it against something big like the Human RefSeq database? If so you are probably familiar with how global tools for peptide spectral match and protein scoring tend to not scale very well for tiny inputs.
BioPharma Finder is specifically designed for much smaller inputs for this reason. I've been looking for a good free tool that can do the stuff that BPF can and I haven't had much luck yet, but there are still nearly 1,000 proteomic software tools to check!
This new study at ACS digs into the gap between small sample input and database size specifically for DIA. By optimizing the database to reflect the sample, everything gets better!