Coupling of protein HPLC to MALDI-TOF MS using an on-target device for fraction collection, concentration, digestion, desalting, and matrix/analyte cocrystallization

Multidimensional protein chromatography offers an alternative to gel-based separations for large-scale proteomic analyses of highly complex mixtures. However, these liquid separations divide the original mixtures into multitudes of discrete samples, each of which may require numerous steps of sample manipulation, such as fraction collection, buffer exchange, protease digestion, peptide desalting, and, in the case of MALDI-MS, matrix and analyte cocrystallization on target. When traditional high-flow liquid chromatography is used, large volumes of solvent must also be removed from fractions to maximize MS sensitivity. Although robotic liquid-handling devices can facilitate these steps and reduce analyst/sample contact, they remain prototypic and expensive. Here, we explore the use of a novel, one-piece elastomeric device, the BD MALDI sample concentrator, which affixes to a MALDI target to create a prestructured 96-well sample array on the target surface. We have developed methodologies to process high-flow HPLC fractions by collecting them directly into the elastomeric device and then subjecting them to sequential on-target sample concentration, buffer exchange, digestion, desalting, and matrix/analyte cocrystallization for MALDI-MS analyses. We demonstrate that this methodology enables the rapid digestion and analysis of low amounts of proteins and that it is effective in the characterization of an HPLC-fractionated protein mixture by MALDI-TOF MS followed by peptide mass fingerprinting.