"Versalinx Microarray Technology - a Novel Platform for Protein Microarray Assays Based on a Synthetic Affinity Binding System" by Anna Gall, ProLinx agall@prolinxinc.com

An emerging technology that holds significant promise for
the high throughput structural and functional 
characterization of the complex components of proteomes
is protein microarrays. Due to the diverse and fragile 
nature of proteins, however, tools and technologies which
found success in DNA arrays cannot be directly adapted 
to attachment of proteins to array substrates. Prolinx*, 
Inc. has developed a protein array platform based on its 
proprietary VersalinxTM Chemical Affinity Tools. The 
platform consists of 3 x 1 inch glass slides coated with a 
3D-polymeric structure containing salicylhydroxamic acid 
(SHA), and a set of protein conjugation reagents based on phenyl(di)boronic acid (P(D)BA). Modification of proteins 
with P(D)BA is done in solution, independent of the 
immobilization step, and can be rapidly optimized to 
retain protein activity. 3D SHA surface produces arrays 
with excellent spot morphology and very low non-specific 
binding without requiring blocking. Our data indicates that
this array technology offers unprecedented utility and 
flexibility, and is compatible with high throughput 
automated array preparation and existing microarray 
spotting and detection instrumentation.

Surface plasmon resonance is a powerful, sensitive and 
label-free methodology for the analysis of biomolecular 
interactions. However, the utility of this technology has 
been limited by the cost, throughput, and complexity of 
available instrumentation and surface chemistries. 
Prolinx®, Inc. has developed a new SPR-based 
instrument, the Octave(tm) Molecular Interaction Analysis 
System, which will address these limitations and will 
enable SPR biosensors to become ubiquitous in life 
science research and drug discovery laboratories.  This 
platform is the result of combining the Texas Instruments 
Spreeta® 2000 chip with Prolinx Versalinx(tm) Chemical 
Affinity Tools. The Octave incorporates eight independent 
sensors operating in parallel allowing analysis of up to 
eight samples and controls in a single run. The gold 
sensor surface has been modified to minimize nonspecific 
binding and utilizes Versalinx Chemical Affinity Tools to 
facilitate the immobilization of macromolecular ligands for 
binding studies. Samples are introduced to the sensors 
using an integrated automated liquid handling instrument, 
enabling walk-away analysis. The versatility and ease of 
use of the Octave provide affordability and accessibility of 
molecular interaction analysis for both academic and 
industrial laboratories.

"Complimentary identification of protein digests using a combined MALDI and ESI dual source Q-Tof mass spectrometer" by Richard Tyldesley, Micromass richard.tyldesley@micromass.co.uk

Protein identification by mass spectrometer is now a routine in many biochemistry laboratories. There are several alternative methods for producing an identification of an unknown protein, but these nearly always require the mass measurement of peptides. The analysis of the peptides is typically performed by either ESI or MALDI. These two ionisation techniques have until now always been performed on different types of mass spectrometers. In this presentation we compare the MS and MS/MS spectra from the analysis of protein digests using ESI and MALDI on the same instrument. This is now possible using the dual source available on the Q-Tof mass spectrometer. The two ionization techniques are known to produce different MS and MS/MS spectra from the analysis of the same sample. In this poster we investigate these differences and illustrate their complimentary nature for protein identification using database searching and bioinformatics.

"A Parallel Column LC-MS/MS System" by James Langridge, Micromass 
james.langridge@micromass.co.uk

The need for high sample throughput whilst maintaining good chromatographic resolution and high sensitivity is a primary goal in large scale proteomics laboratories utilising LC-MS/MS. A typical experiment might involve trapping a protein digest sample onto a small cartridge column for desalting: the desalted sample is then eluted onto an analytical column and subjected to a full reverse phase gradient. Chromatographic resolution and high sensitivity is achieved using nanoscale analytical columns, operating at 200 – 400 nL/min flow rates. Any reversed phase LC-MS/MS run will involve a column re-equilibration step after the gradient has been completed, where a highly aqueous solvent is flushed through the column to prepare it for the next injection. This consequently leads to a 'dead time' in the experiment during which no data can be acquired by the mass spectrometer. The removal of this dead time would lead to a reduction in the total experiment time, especially when large numbers of samples, for example, contained in a 96 well microtitre plate are to be analyzed. We describe an experimental arrangement where two sets of analytical and trapping columns are operated in parallel. This allows the time required for re-equilibration for one set of columns to be absorbed into the elution step for the opposite set of columns. The system uses a ternary solvent delivery system, a single ESI spray tip and two switching valves. One of the valves has an extremely low internal volume, which is essential for its use post column to reduce peak broadening. This arrangement allows two samples to be analyzed in less than one hour - including injection time - while running a 25-minute gradient for each sample.