Can anyone tell me the largest number of proteins directly extracted from soil ?
I am writing a paper about soil protein extraction and wanted to know what sort of yields other researchers were getting and where my results would fit in. I was sampling a Silty Clay Loam grassland soil and extracted around 1500 proteins. I have found a few references to the Hultman multiomic Antarctic Bog soil and another to the paper by Callister on a prairie soil metaproteome. Would my extract number be high for temperate grassland soils ?
Here is some clue....
Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics
J. Proteome Res. 2010, 9, 12, 6615-6622, https://doi.org/10.1021/pr100787q
Abstract : We present a novel direct protocol for deep proteome characterization of microorganisms in soil. The method employs thermally assisted detergent-based cellular lysis (SDS) of soil samples, followed by TCA precipitation for proteome extraction/cleanup prior to liquid chromatography−mass spectrometric characterization. This approach was developed and optimized using different soils inoculated with genome-sequenced bacteria (Gram-negative Pseudomonas putida or Gram-positive Arthrobacter chlorophenolicus). Direct soil protein extraction was compared to protein extraction from cells isolated from the soil matrix prior to lysis (indirect method). Each approach resulted in identification of greater than 500 unique proteins, with a wide range in molecular mass and functional categories. To our knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures. This protocol should provide a powerful tool for ecological studies of soil microbial communities.
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