I have a long list of peptide sequences which I would like to look up in batch mode in public sources/ databases, to see if the peptides have been identified as biomarkers in specific tissues (plasma, urine, etc). The problem is that the peptides have been generated using a trypsin digest, which means that I do not always get exact matches and need to also find inexact matches to my peptide queries by finding cases with irregular digest cleavages. It would also be helpful to identify the parent/target protein(s) the peptide may be coming from if it's an accurate/reliable method. When I looked for this, the only R packages I am finding that can handle issues with enzyme digests deal with spectra rather than peptide sequences. I would appreciate any suggestions on how to do this, thanks!
Does anyone have any suggestions on how to automate looking up exact peptide sequences in public sources/ databases to see if the peptides have been identified as biomarkers with an R script?