The First International Conference of the Hellenic Proteomics Society took place at the Foundation for Biomedical Research of the Academy of Athens, Athens, Greece, 22-25 May 2005. Scientists from about 20 countries attended this conference where proceedings in proteomics methodologies, advances in mass spectrometry, proteomics applications, disease diagnostics and bioinformatics were presented. The relatively small size of the meeting gave the opportunity for the attendees to interact and discuss projects and collaborations. The event was completely financed by companies which exhibited their products and services related to proteomics research.