The blood-feeding invertebrates are a rich biological source of drugs and lead compounds to treat cardiovascular diseases because they have evolved highly efficient mechanisms to feed on their hosts by blocking blood coagulation. In this work, we focused our attention on the leech Hirudo medicinalis. We performed, by "intensity fading" MALDI-TOF mass spectrometry, a comprehensive detection and functional analysis of pre-existent peptides and small proteins with the capability of binding to trypsin-like proteases related to blood coagulation. Combining "intensity fading MS" and off-line LC prefractionation allowed us to detect more than 75 molecules present in the leech extract that interact specifically with a trypsinlike protease over a sample profile of nearly 2,000 different peptides/proteins in the 2-20-kDa range. Moreover we resolved 232 individual components from the complex mixture, 13 of which have high sequence homology with previously described serine protease inhibitors. Our findings indicate that such extracts are much more complex than expected. Additionally, intensity fading MS, when complemented with LC separation strategies, seems to be a useful tool to investigate complex biological samples, establishing a new bridge between profiling, functional peptidomics, and subsequent drug discovery.
Molecular & Cellular Proteomics 4:1602-1613, 2005.Although the task of identifying and characterizing genes in many sequenced genomes in the last years has been very intense, it is even more challenging when applied to the much higher complex field of the protein world (1). One difficult set of proteins for such analysis are those which we could term as "small" (i.e. below 15-20 kDa) (2) because of their variety and difficulty to be detected by several established proteomic approaches such as 2D 1 electrophoresis (3) or computational genomic scanning (4) among others. Therefore, the development of efficient and high throughput technologies for producing functionally related data of peptides and small proteins (2-20 kDa) is increasingly attracting attention. Some of these proteins have potential use for diagnostics or therapeutics (5-7). They include families of peptide hormones, neuropeptides, cytokines, growth factors, and enzyme inhibitors acting as biochemical messengers or modulators that organize the regulatory processes in all organisms (6). In fact, most of the important biopharmaceutical products approved for therapeutic applications are molecules within a molecular mass range of 1-40 kDa (8).The proteomic strategy focused on the analysis of peptides and small proteins from complex mixtures has been named "peptidomics" (9, 10). The primary proteomic tool, 2D gel electrophoresis with mass spectrometry, has been gradually enhanced, and sometimes replaced, by three main technologies: MALDI MS in combination with LC (off line) (9, 11, 16), ESI MS combined with nano-LC (on line) (12-16), and MALDI-TOF MS for in situ peptide profiling (17-21).One of the main goals of these technologies is to provide a compre...