the variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. the subcellular and biochemical fractionation resulted in Go term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress. Tomato (Solanum lycopersicum L.) is a crop of high economic and nutritional value produced worldwide and the most widely used model to study different aspects of development and ripening of fleshy fruits 1. Fruit ripening coincides with seed maturation in the final phase of fruit development and is a highly coordinated, genetically programmed, irreversible phenomenon involving a series of physiological, biochemical, and organoleptic changes that lead to changes in colour, texture, flavour, aroma, and nutritional status 2. It is coordinated by drastic hormonal changes and, although ethylene is considered the major hormonal regulator in climacteric fruit ripening, other hormones such as auxin and abscisic acid (ABA) take part in this process 3. During fruit development, the concentration of carbohydrates, amino acids, and organic acids diminishes immediately after fruit setting and is partially recovered during fruit ripening 4 with increased sugar levels, starch hydrolysis, decreased acidity 1 , pulp softening 5 , aromatic component and color development 6. The tomato genome has been recently sequenced and annotated 7 and a number of post-genomic approaches have been used to gain insights into molecular networks controlling fruit development and ripening 8. High-throughput proteomics analyses were reported recently 9-13. Moreover, analyses of fruit transcriptomes 14,15 and metabolome 16,17 as well as multilevel studies integrating transcriptomics and metabolomics 4,18,19 , transcriptomics and enzyme profiles 20 , or transcriptomics, proteomics, and metabolomics 8,21 have been performed. These studies have provided an enormous amount of data that expands our knowledge of the molecular events associated with ripening. While many enzymes are soluble proteins, membrane-spanning or membrane-associated proteins are more challenging to proteomic analysis 22. In this work, we obtained a proteo...