Metaproteomic studies of whole microbial communities from environmental samples 
(e.g., soil, sediments, freshwater, seawater, etc.) have rapidly increased in 
recent years due to many technological advances in mass spectrometry (MS). A 
single 24-h liquid chromatograph-tandem mass spectrometry (LC-MS/MS) measurement 
can potentially detect and quantify thousands of proteins from many dominant and 
subdominant naturally occurring microbial populations. Importantly, amino acid 
sequences and relative abundance information for detected peptides are 
determined, which allows for the characterization of expressed protein functions 
within communities and specific matches to be made to microbial lineages, with 
potential subspecies resolution. Continued optimization of protein extraction 
and fractionation protocols, development of quantification methods, and advances 
in mass spectrometry instrumentation are enabling more accurate and 
comprehensive peptide detection within samples, leading to wider research 
applicability, greater ease of use, and overall accessibility. This chapter 
provides a brief overview of metaproteomics experimental options, including a 
general protocol for sample handling and LC-MS/MS measurement.