The NCI-60 is one of the most well used collections of cell lines in the world. There are cell lines from nearly every main cancer type and they have been studied in a remarkable number of ways over time. Everything from drug sensitivity to radiation resistance...somebody's done it. And the NCI has painstakingly maintained correct back-frozen freezer stocks so everyone knows they are doing the right things.
This dataset is perfect for meta-analyses. Case in point, this new paper in JPR this month from Maria Karapova et al.,. In this study they go back through shotgun proteomics data that they acquired on these cell lines and compare those to FASTA database files generated from whole exome sequencing. This gave them a direct way of comparing the transcriptome of these cells to the proteome and boost their matches through the ceiling.
Awesome study that shows how much data we're missing if only we figure out a way to really search for it!
The sequential database search question is interesting. Maybe it's not OK to give all the proteins in your database the same initial probability. Reminds me of the PLOSone paper by Alexey L. Chernobrovkin and Roman A. Zubarev (2014).
ReplyDeleteThey only find some 200 extra peptides per sample though. It's through the ceiling maybe but not through the roof!