Bioinformatic limitations are seriously affecting
This new study shows how big the problem is -- and provides a way to accurately assess how your search parameters are affecting your results!
They do some glycoproteomics on samples of different complexity while spiking in the same protein, AGP1.
A quick Google Image search says....this is AGP-1...thats a bunch of glycans! Now that they have a good control glycoprotein, they can see how changing the search parameters affect their ability to detect the glycopeptides they know are there.
And the results are....scary. In the most complex samples if they just do a "naive" search where the search engine is looking for any possible glycosylation sites or combinations....the likelihood that they can find their control glycopeptides diminishes to almost zero.
Take away from this study?
1) More specific (informed) searches are going to be a whole lot better for more global studies AND
2) Having a good control like this AGP-1 protein is a great way to make sure you're on the right track!!