Proteomics of secretory vesicles, perspectives:

As shown in this review, the different proteomic analysis of secretory vesicles performed so far, allowed to identify several new proteins for each type of secretory vesicles. This approach has permitted to obtain new information concerning the biogenesis and the exocytosis mechanisms of secretory vesicles. The study of quantitative or qualitative modifications of secretory vesicle proteome after treatment with drugs or secretagogues could also be an interesting alternative strategy to highlight new proteins involved in the modulation of cell secretion.

2.8.1. Protein quantitation:

Recently, several labelling methods have been developed to directly perform relative quantitation of identified proteins in mass spectrometry [130, 131]. SILAC has been specifically developed for in vivo labelling of cultured cells [132]. This method

consists to cultivate two similar cell populations either in normal cell culture condition or with a culture media where one essential amino acid is replaced by an isotopically heavy form that is incorporated in nascent proteins. In a next step, each cell population can be exposed to different stimuli. The two cell populations are mixed and secretory vesicles can be isolated through one of the previously discussed isolation methods. Secretory vesicle proteins can be then identified by mass spectrometry. In addition, heavy and light amino acids can be easily distinguished in mass spectrometry, which allow to detect any modification of protein expression, due to cell stimuli. So far, SILAC approach has been very rarely used to quantitatively compare the proteome of secretory vesicles isolated from cells treated with different stimuli, probably because this method is relatively new and require the acquisition of expensive mass spectrometers. However, SILAC and mass spectrometry represent extraordinary tools to compare in a quantitative manner the proteome of secretory vesicles, exposed to different cell culture conditions. It will thus allow to test the effect of different drugs and secretagogues on the modification of the proteome of secretory vesicles, which could potentially explain the modulation of secretion induced by these compounds.

Other types of protein labelling have been developed for protein quantitation, such as iTRAQ [133] or TMT [134]. In this case, each protein population is chemically labelled with an organic compound of a known mass. The addition of these compounds does not affect the behaviour of the labelled proteins in a mass spectrometer. The fragmentation of the labelled protein in MS/MS mode induces the release of the protein tag corresponding to one specific protein population. The comparison of the intensity of the fragmented tags from different protein populations allows to compare the expression of proteins coming from different biological samples. The main

advantage of this type of protein quantitation is that it enables to compare up to 10 different samples.

2.8.2. Protein post translational modifications:

It is known that post-translational modifications (PTM) are able to modulate activity of most eukaryotic proteins [135]. Therefore, PTM mass spectrometry detection of secretory vesicle proteins after drug or secretagogue cell stimulation, could certainly allow to better understand some of the mechanisms governing modulation of cell secretion. So far, many different PTM have been highlighted, such as phosphorylation, glycation, glycosylation, acylation or ubiquitination [136]. As peptides triggering PTM have more difficulties to be analyzed by mass spectrometry compared to non-PTM peptides, it is often necessary to enriched proteins with a specific PTM, for their efficient detection in mass spectrometry. Several chromatographic columns have been developed to specifically enriched proteins and/or peptides with one particular PTM, such as phosphorylation with IMAC [137]

and TiO2 columns [138] or glycation with boronate columns [139]. The detection of PTM by mass spectrometry is based on the loss of the PTM during peptide fragmentation, which corresponds to a specific ǻmass. Once detected, peptides triggering PTM can be identified. It is also possible to quantify proteins with PTM by using the SILAC strategy. This approach has been used to identify and quantify phopshoproteins from unstimulated and EGF-stimulated cells [136]

2.8.3. Bioinformatics:

Performant mass spectrometry software are necessary for the quantification of proteins and detection of PTMs [140]. However, the main mass spectrometry softwares such as Mascot, Phenyx, Profound or Sequest have been initially developed only to obtain identification of proteins either by PMF or MS/MS. The recent development of efficient mass spectrometers allowing the detection of PTM and/or the quantification of proteins opened an urgent need for the development of new bioinformatics tools allowing the management of PTM and protein quantitation after mass spectrometry analysis. recently, several mass spectrometry software have began to be upgraded in order to be able to automatically detect mass shifts corresponding to a particular PTM or to the labelling of peptides with isobaric tag or isotopic amino acids [141]. However, due to the large numbers of different PTM and quantification methods, the development of more specific bioinformatics tools will be necessary in the future.

3. CONCLUSION:

The comprehension of the mechanism governing cell secretion is fundamental since this process allows the release of endocrine, paracrine or autocrine compounds.

Secretory vesicles are the key organelles of this secretory pathway. Due to the high number of different secretory vesicles, only few of them have been studied in detail so far. However, as described in this review, the combination of subcellular fractionation, proteins separation and mass spectrometry analysis, recently allowed to establish the partial proteome of a wide range of secretory vesicles. All proteomic studies of secretory vesicles allowed to identify several hundreds of proteins that are often present in different types of secretory vesicles. However the knowledge of the

specific protein content of each secretory vesicle may represent the starting point for further biological analysis and could potentially succeed to obtain a better comprehension of the cell secretion mechanisms of each type of cell. In addition, quantitative and/or qualitative comparisons of the secretory vesicle proteome isolated from cells that have been treated with different drugs or secretagogues, will also certainly allow to better understand some impairments of cell secretion.

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