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BackgroundJatropha curcas(Euphorbiaceae) is cultivated for harvest-ing the unique oil contained in its seeds, which can beused as raw material for the production of biodiesel [1].The seed cake remaining after pressing can not be usedfor animal feed, because it contains toxic proteins andother compounds, e.g. curcin, phorbol esters. The devel-opment of genotypes better suited for the production ofbiodiesel showing lower levels of toxic/allergenic pro-teins is being hampered by a lack of understanding thea) metabolic pathways and enzymes leading to the pro-duction of fatty acids during seed development and b)role of proteins deposited during seed development. Inrecent years the field of proteomic research has becomea fast growing discipline with high relevance to biologi-cal sciences.While genomic and transcript-profiling studies haveprovided a wealth of information about different plantdevelopmental processes, there is growing awarenessthat the abundance of mRNA transcripts is not alwaysrepresentative of protein levels and that mechanisms ofpost-translational regulation must also play an impor-tant role.Proteomics is a systems biology based approach inves-tigating the whole expressed proteins at a given timepoint and under certain condition [2]. It has beenshowntobeavaluabletoolforstudyingthebiologyofliving organisms and their interaction with the environ-ment in post genomics area. Proteomics has beenshown to have potential values to deliver knowledgeabout complex biochemical processes and is being usedin various fields of modern botany and agriculture likeplant biomarker discovery related to resistance as wellas drought and water stress. Furthermore proteomicsoffer major advantages linked to its high throughputcapacity and its ability to perform simultaneously theanalysis of hundreds of proteins from the same samples.MethodsThe method of choice for proteome analysis is the com-bination of high resolution protein separation like twodimensional gel electrophoresis (2-DE) with tandemmass spectrometric (MS/MS) identification of proteins.The two dimensional gel electrophoresis separatesproteins based on their isoelectric points (isoelectricfocusing)andinaseconddimensionbasedontheirmolecular weight [3].In this study a proteomic approach was conducted inorder to identify the expression patterns of interestingproteins during seed development, as well as toxic and/or allergenic proteins in Jatropha, 2-DE coupled withmass spectrometry and de novo sequencing, wereemployedto analyze whole seed proteins of six develop-mental stages, covering the essential ontological phasesof these important plant organs.Prominent spots identified in 2-DE analyses wereexcised, washed, reduced with DTT and alkylated withiodoacetamide. The in-gel digest with trypsin was car-ried out for 8 hours. The peptides were de-salted usingµZip-Tips C18 (Millipore) and 0.5 µl were spotted ontoadisposableAnchorChipMALDItargetplatepre-spotted with a-cyano-4-hydroxycinnamic acid (PAC tar-get, Bruker Daltonics). Data were acquired on a MatrixAssisted Laser Desorption Ionisation Tandem Time-of-Flight (MALDI-TOF/TOF) mass spectrometer (UltraflexII, Bruker Daltonics) in MS and MS/MS modes. Spectraprocessing and peak annotation were carried out usingFlexAnalysis and Biotools (Bruker Daltonics).In order to enhance the quality of tandem mass spec-trometry (MS/MS) spectra for de novo sequencing,

Proteomics, a systems biology based approach to investigations of Jatropha curcasseeds