Anti-clogging device and method for in-gel digestion applications

#Matrix-assisted laser desorption/ionization (MALDI) analysis is a useful tool for solving structural problems in biochemistry, immunology, genetics and biology. Samples are ionized and a time of flight (TOF) analyzer is used to measure ion masses. TOF analysis begins when ions are formed and are accelerated to a constant kinetic energy as they enter a drift region. They arrive at a detector following flight times that are proportional to the square root of their masses. A mass spectrum is created because ions of different mass arrive at the detector at different times.

#Mass spectrometry can be a particularly powerful tool in the fields of drug discovery and development, genotyping, and proteome research. Current trends in research are to analyze larger and larger numbers of samples using automated handling equipment or robotics. Quantities of individual samples are from the nano-mole levels to femto-mole levels. As a result, instrumentation is becoming more sensitive and a need exists for sample handling formats to be miniaturized, high density and disposable.

#In-gel digestion of protein is a proteomics method that has many sample preparation steps prior to sample analysis (such as by MALDI TOF MS). Briefly, upon separation in the electropherisis gel, the proteins in a sample are stained for detection and portions of the gel containing the protein of interest are excised. The stain is then removed from these gel portions, and an enzyme solution is used to selectively digest the protein sample to form peptides that migrate out of the gel portion into solution. After purification of the peptides, analysis of the sample is carried out.

#FIG. 1 is a perspective view of a single well for a multiwell sample preparation device in accordance with the present invention;

#FIG. 2 is a perspective view of a single well for a multiwell sample preparation device shown containing a gel piece in accordance with the present invention;

#FIG. 3 is a cross-sectional view of a single well for a multiwell sample preparation device shown containing a gel piece in accordance with the present invention;

#Suitable substrate materials for the sample preparation device of the present invention are not particularly limited, and include plastics (such as polyethylene and polypropylene), glass and stainless steel. The substrate materials should not interfere with the operation of the device or the chemicals to be used in the procedure. Polyolefins, and particularly polypropylene, are preferred materials.

#Turning now to FIGS. 1 and 2, there is shown generally at 10 a single well 12 suitable for use in a single well or a multiwell sample preparation device that has a plurality of wells. A well 12 is defined by a vertically extending fluid impervious side wall and a sloping bottom portion. The middle and upper portions of the well 12 preferably have a uniform diameter and are substantially cylindrical in cross-section, although other configurations are contemplated and within the scope of the present invention. The lower portion of the well 12 tapers downwardly, in the direction of fluid flow, towards a bottom portion 13, which slopes inwardly towards a center, thereby having a frusto-conical configuration. Bottom portion 13 has a drain 15 that is preferably centrally located in the well 10.

#Formed in the bottom portion 13 of the well 10 are one or more fluid passageways 18. The fluid passageway(s) 18 modify the otherwise relatively smooth or even surface of bottom portion 13 and effectively provide a gap or space between a sample carrier 20, such as a gel piece (FIG. 2), that is contained in well 12 and supported by the bottom portion 13, and the drain 15. The sample carrier can be a liquid but is preferably a solid, such as a gel, coated bead or a membrane. In order to insure fluid flow between the well 12 and drain 15 when the carrier 20 is present in the well 12, the smallest dimension of each passageway 18 should be less than the smallest dimension of the carrier 20, so that the carrier 20 cannot be positioned in the passageway 18 to block fluid flow into the drain 15. In this way, at least a portion of the fluid passageway(s) 18 is always in fluid communication with the drain 15 and cannot be blocked or clogged by a carrier 20 when placed in the well 12, as exemplified by illustration in FIGS. 2, 3 and 4. Where the carrier is a gel piece, it is noted that typically circular plug cutters found in automated picker robots cut the gel portion uniformly. However, the present invention is not limited to uniformly-shaped carriers, as the fluid passageway(s) 18 are configured to prevent fluid blockage even when carriers of irregular shape are present in the well 12. For example, a single slit that is longer than the carrier is within the scope of the present invention.