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What kinds of detergent-free bacterial lysis buffers exist? The proteins we're extracting will be later analyzed by LC-MS/MS, and we're looking for a lysis buffer that won't interfere with this downstream analysis.

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I'm a HUGE fan of FASP (filter-aided sample preparation) which is an in-solution preparation/digestion. It is very fast, allows you to not worry about a protein precipitation step, and gets rid of all MS incompatible substances with the wash steps (so doesn't matter what lysis buffer you use). It requires very few, inexpensive materials (a pack of 100 centrifuge filter units is less than 250 USD from VWR) and has great recovery. This is the link to the Nature Methods paper that the linked protocol is based on (the linked protocol is an updated, faster version of the Nature Methods one).

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There are a few techniques available for this.

Some recommend a urea-based technique, others recommend a chloroform. Do you have more information about your specific needs?

A Chloroform-Assisted Protein Isolation Method Followed by Capillary NanoLC-MS Identify Estrogen-Regulated Proteins from MCF7 Cells

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why not use a french press? put a few thousand PSI on the sample and the cells just pop open. The lysis buffer contains no detergents:

Lysis buffer:
50 mM Tris-HCl pH 7.5
50-200 mM NaCl*
1 mM MgCl2
5 mM DTT
1 mM PMSF

the salt concentration is variable and you could probably do without the DTT too if thats a problem ...

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