Are you considering venturing into the scary dark world of metaproteomics?! Do you have no choice, cause no one has sequenced your darned organism yet -- or all of the organisms in your darned sample?!?
You probably want to check out this cool new (open access) insight paper.
This is a nice beginner's guide to the field -- what you need to worry about, where you're going to run into problems, etc.,
It is a short read and looks like a quick overview until you get into the Supplemental info which adds some depth to it. Quote I find interesting:
MS-based metaproteomics is now practical due to advances in duty cycle and increased mass accuracy for both precursor and fragment masses. These improvements allow for the detection of over 104 tandem mass spectra from a single data-dependent acquisition MS analysis of a mixed microbial sample.
Maybe it's a little dated, considering how many files I'm seeing with 1e5 MS/MS spectra per run, but accurate MS1 and MS/MS masses sure do take a lot of uncertainty out of...well...a lot of uncertainty!
Stellar little review on a crazy complex -- and rapidly growing -- field!
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