What are all these un-matched spectra? Does this keep you up at night, or do I just have insomnia and an odd sense of priorities? Sometimes I get data sets to look at where Sequest can only explain 10% of the MS/MS spectra. Normally this is on weird organisms, but with human cells it isn't that odd for only 30% to match the database. Sure, I can dump them through Preview and figure out what PTMs to go after and use multiple engines, and other techniques to push these numbers up.
At the end, however, we are searching our data against a translated and extremely conservative DNA sequence. If the DNA that was present really was what made it to the protein level, then what the heck are all these genomics and transcriptomics people doing all day? The fact of the matter is that the coding in the DNA gets mixed up, flipped around and sometimes spliced together before it becomes RNA or protein. At this point, we simply have to ignore a lot of this.
SPLICEPROT is an attempt to go after some of the products of nucleotide sequence splicing. It has a nice web-based interface to construct a database that you will be able to search with existing tools for splicing events.
You can read about this algorithm here.
And you can actually take a swing at SPLICEPROT here.
Thanks to Pastel BioSciences for the link to this one.
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