Recent interest in proteomic approaches within the fungal biology domain led to an increased number of publications using this technique (as reviewed in Kim et al., 2007). Methods for protein extraction rely on a combination of extraction procedures; they are often scarcely described in the methodological sections and require expertise in dealing with the potential troubleshooting methods.

As for other "omics" approaches, setting standards for sample and data processing is essential in order to generate reliable scientific information. Moreover samples and procedures of manipulation should be adequately described in order to allow shared result interpretation among different "omics" experiments. This would be essential for fully exploiting potentiality of cross-data mining in genomics, proteomics, metabolomics, ... (Morrison et al., 2006). Minimum information about a proteomic experiment has been drafted and working groups have been established in order to tackle all the aspects of an experiment (Gel electrophoresis, Mass Spectrometry, Molecular Interactions, Protein Modifications, Proteomics Informatics, Sample Processing). At the moment no defined information are available on sample processing procedures. Given the importance of protein extraction procedures in determining the final quality of proteomic studies, in order to implement procedures that can increase standardization within the framework of MIAPE guidelines (Taylor et al., 2007), we proposed the use of a video protocol detailing sample processing. Video description of experiments may contribute substantially to increase the number of information on sample processing that may result in better reproducibility of "omics" experiments (Pasquali, 2007).

Indeed, reproducibility across laboratories is a fundamental requirement in order to guarantee validity of proteomics results (http://www.fixingproteomics.org). The cross-laboratory reproducibility is influenced by two factors: different instrumentations and different operators manipulating samples.

In the described protocol, we propose to perform biological replicates involving multiple operators (Figure 2 and video) to increase the reliability of data (i.e. technical variation of the results is taken into account).

The procedure described for protein extraction is based on SDS and heating. This was previously shown to guarantee a good purity and quantity of proteins (Bridge 1996). SDS coupled with boiling dissolves cell walls, hydrophobic proteins and prevents the formation of oligomers that abort precipitation of proteins. Boiling allows also inactivation of proteases. The same effect is produced also by EDTA, PMSF and complete mini protease inhibitor. DTT removes disulfide bridges in and between proteins facilitating protein solubilization.

In order to remove SDS before IEF, proteins are precipitated by acetone/TCA/DTT. Furthermore, acetone/TCA/DTT precipitation allows removing some contaminants such as lipids, nucleic acids, salts or/and phenolic compounds when these compounds are present. Like SDS, these molecules prevent a good migration during IEF. Following this precipitation, it is necessary to wash the precipitated proteins by acetone/DTT, in order to remove TCA as it can interfere with IEF.

A good sample preparation is the key to good results. For this, it is also essential to avoid contamination of proteins from the environment working with powder free gloves and respecting good laboratory practices. From a technical point of view, within the described protocol, the most critical steps for obtaining sufficient amounts and purity of proteins are two phases. First, the grinding phase where complete destruction of the cell is fundamental to release proteins; and second, the purification of total proteins, a phase encompassing the removal of the majority of lipids, DNA and other contaminants that may interfere with the migration of proteins.