Parameterized algorithms for hitting set variants applied to protein identification in shotgun proteomics

Abstract: This work is dedicated to problem of protein identification in bottom-up proteomics, and in particular, in shotgun proteomics. It is aimed on providing a new way of interpretation of peak lists. Several computational problems are outlined and it is shown by simulations that despite NP-hardness, the problems in question can be relatively fast solved for practical cases. Problems are also studied from parameterized complexity theory perspective.