Sample Preparation for MALDI Mass Spectrometry Using an Elastomeric Device Reversibly Sealed on the MALDI Target

Abstract

A new method for improving low-concentration sample recovery and reducing sample preparation steps in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is presented. In the conventional approach, samples are typically desalted and/or concentrated with various techniques and deposited on the MALDI target as small droplets. In this work, we describe a new approach in which an elastomeric device is reversibly sealed on the MALDI target to form a multi-well plate with the MALDI target as the base of the plate. The new format allows a larger volume (5-200 microL) of samples to be deposited on each spot and a series of sample handling processes, including desalting and concentrating, to be performed directly on the MALDI target. Several advantages have been observed: (i) multiple sample transferring steps are avoided; (ii) recovery of low-concentration peptides during sample preparation is improved using a novel desalting method that utilizes the hydrophobic surface of the elastomeric device; and (iii) sequence coverage of the peptide mass fingerprinting map is improved using a novel method in which proteins are immobilized on the hydrophobic surface of the elastomeric device for in-well trypsin digestion, followed by desalting and concentrating the digestion products in the same well.

Evaluation of an on‐target sample preparation system for matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry in conjunction with normal‐flow peptide high‐performance liquid chromatography for peptide mass fingerprint analyses

“…A novel 96‐well elastomeric sample preparation device has recently been developed which seals directly to the surface of a MALDI target creating, in effect, a 96‐well plate on its surface capable of holding solution volumes of up to 200 µL of solvent 38. Sample preparation is performed in a similar way to that used for normal MALDI sample preparation, with the exception that the large volumes of solvent may be evaporated off of the MALDI target using a SpeedVac™.…”

“…Prototype 96‐well elastomeric devices were obtained though a collaborative effort with BD Biosciences. Different generations of the device were tested, all in 96‐well format, compatible with the Bruker Daltonics standard MALDI target design, which varies slightly in design and format from the ABI target format recently described by Chen et al 38. As these prototypes were prepared manually in a pre‐commercial manufacturing process, it was necessary to subject them to a cleaning protocol.…”

“…Recently, a novel sample preparation device, the BD™ MALDI sample concentrator, has been developed. This simple, inexpensive (non‐robotic and reusable) 96‐well elastomeric array may be directly sealed onto the surface of a MALDI target in order to create an on‐target 96‐well plate capable of processing samples for MALDI‐TOFMS 37–40. The sample preparation is similar to that for standard MALDI, with the exception that the large volumes of solvent are now evaporated directly off of the MALDI target via a SpeedVac™ (Thermo Electron, Waltham, MA, USA).…”

DNA methyltransferase expression in the mouse germ line during periods of de novo methylation

“…The polymeric plate developed in this study was also characterized by the presence of hydrophobic domains introduced to induce sample confinement in the enzyme‐active areas (Ibáñez et al, 2007). In another report, Chen et al (2006) described an approach in which an elastomeric device was reversibly sealed onto the MALDI target: it was noted that proteins could be readily immobilized on the hydrophobic surface of this elastromeric device and the in‐well tryptic digestion performed (Chen et al, 2006; see also Table 1).…”

Lab‐on‐a‐plate: Extending the functionality of MALDI‐MS and LDI‐MS targets

“…The polymeric plate developed in this study was also characterized by the presence of hydrophobic domains introduced to induce sample confinement in the enzyme-active areas (Ibáñez et al, 2007). In another report, Chen et al (2006) described an approach in which an elastomeric device was reversibly sealed onto the MALDI target: it was noted that proteins could be readily immobilized on the hydrophobic surface of this elastromeric device and the in-well tryptic digestion performed (Chen et al, 2006; see also Table 1). …”