This isn't anywhere near a complete list, but if you're finding yourself motivated to jump into virus proteomics all the sudden for some weird reason or the other, here are some awesome resources.
This review is where everyone (IMHO) should start.
If you're looking for something beyond what the 137 references in that paper can provide, you might need to do some jumping jacks.
However, if you wanted to focus on specifically LCMS methods for virus stuff, a really good next stop would be going to Google Scholar and typing in Virus and Arthur Moseley. That team at Duke has been getting DARPA funding to work on virus detection for years (that's who is acknowledged in at least some of the papers).
In this one they identify host targets using 2D-wait...gels...?...hey, it works and then they build targeted assays for the host biomarkers.
And this one is my current favorite. In this one they build targeted assays for viral proteins!
The peptides are hunded down with an LC-QTOF and LC-MRM (all Waters instruments) are developed. Stable isotope peptides are used for the MRMs and 30 minute NanoLC gradients.
On the TQ-S they get theoretical LODs in the sub-femptomol range!
AND they show that they can use targets for the variable regions of the nucleocapsids to work out the lineage of the virus.
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