There is a lot of proteomics software out there. Some good and some...not so good. But there is just so much now that sometimes really comprehensive and long standing developments will slip right around your notice. The work of the Tabb lab at Vanderbilt is one of these for me. This lab has been developing and improving their proteomics workflow for quite a while and has a well polished open source package available. This week we ran some phosphopeptide standards though both this package and Proteome Discoverer and this package came up with nearly 75% of the IDs that PD did. If you are interested in an alternative for processing your shotgun proteomics data, this is definitely worth an investigation!
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