ASMS round up

[Doug]

ASMS 2012 was great. I saw tons of interesting talks and posters. But since it's such a big conference I wasn't able to see everything. Please post and tell us about some of the things you found most interesting.

[Doug]

I really enjoyed a poster presented by Jesse Rinehart of Yale University. They had recently published this paper in Science discussing a method for introducing a novel codon into E Coli as well as the required machinery to encode a phosphoserine at any desired residue. This makes phosphorylated recombinant protein expression much more feasible. But we also discussed the many different ways this method could be combined with other synthetic biology approaches to do some really innovative experiments.

[Doug]

There were a lot out of posters on cross-linking methods to detect protein-protein interactions. Some were using crosslinkers with a very labile bond in the linker region such that MS2 broke only that bond and MS3 was used to ID the two interacting peptides. Others just dissociated the linked peptides in the MS2 scan creating a more complicated MS2 spectrum. While these crosslinking methods have been discussed for years, it seemed that this year the projects went beyond just proof of principle to actually looking at isolated protein complexes and even whole cell lysates.

[Craig]

Sangtae Kim of Pavel Pevzner's group at UCSD gave a great talk about MS-GF+ (formerly MS-GFDB), a universal and sensitive search algorithm. The basic idea is that proteomics data used to be very uniform: trypsin, low-resolution CAD, etc. Now people routinely use different enzymes, different fragmentation methods, different mass analyzers for MS/MS, enrichment protocols, etc. MS-GF+ has something like 1700 models for these various types of data. Kim showed very impressive gains over multiple algorithms, including Mascot+Percolator, for several recent datasets, and it is even competitive with spectral library searching. MS-GF+ is free and available at http://proteomics.ucsd.edu/Software/MSGFDB.html.