You have isolated an unknown protein
but no way of obtaining the sequence that codes for it.
We can help you.
In cases where the sequences of potential peptides are not known, de novo sequencing is the only choice left. Traditionally, this was painstakingly done manually, but there are now many software packages which can perform de novo sequencing of MS2 spectra.
De novo sequencing is standard practice for genomics and transcriptomics, but for proteomics it is far from straightforward. Most MS2 spectra are too incomplete or ambiguous to permit unequivocal identification of the parent sequence. Database Searching is usually preferred in this instance.
Like database searching, de novo sequencing is not an error-free process, so here too careful curation is required for trustworthy results. Data quality will benefit from digesting with several complementary proteases in parallel. Sometimes, a first de novo sequencing step can be used to inform a subsequent database search.
Whether you are working with a rare organism or want to know the sequence of an antibody you have no clone for, do not hesitate to get in touch with us.