Probe for mass spectrometry

Abstract

The present invention relates to a probe for the analysis of one or more analytes, particularly proteins or compounds capable of binding or otherwise interacting therewith, by laser desorption / ionisation mass spectrometry, more particularly MALDI MS. It also relates to a protein microarray, a method of producing a protein microarray and a method of analysing a protein microarray. The probe comprises a support having an electroconductive target surface thereon characterized in that the target surface comprises a micro array having a plurality of discrete target areas presenting one or more analyte capture moieties. Each discrete target area has an area of less than 1000 μm2, more preferably still less than 500 μm2, and more preferably still less than 100 μm2.

Description

[0001] The present invention relates to a probe for the analysis of one or more analytes, particularly proteins or compounds capable of binding or otherwise interacting therewith, by laser desorption / ionisation mass spectrometry, more particularly MALDI MS; It also relates to a protein microarray, a method of producing a protein microarray and a method of analysing a protein microarray. [0002] Such a mass spectrometry probe, upon which a microarray has been fabricated, enables interrogation of protein—small molecule interactions in a label-free manner by desorption and ionisation of analytes (e.g. protein, drug or drug candidate, carbohydrate, DNA, RNA or other test molecule). The probe and methods are particularly useful in the drug discovery process, for example in hit series evaluation, lead optimisation, predictive toxicogenomics and metabolite profiling. [0003] Analysis of disease processes and drug effects have traditionally focussed on genomics, whereas proteomics, the study ...

AI Technical Summary

Benefits of technology

[0003] Analysis of disease processes and drug effects have traditionally focussed on genomics, whereas proteomics, the study of the expressed fraction of a genome; offers a more direct analysis of proteins and their inter-action. Proteomics was initially the quantitative and qualitative study of whole cell, tissue, organ or organism protein expression or fractions thereof Often it involves comparing samples of similar biological origin exposed to different conditions or comparing diseased and non-diseased tissue. One advantage of proteomics over genomics is that it allows quantitative identification and analysis of proteins; by contrast, genomics can only predict the presence of proteins on the basis of mRNAs that might be translated into proteins. Furthermore, proteomics can identify posttanslational modification of proteins and can therefore draw conclusions about the activity of proteins rather than merely describing its presence.

[0028] Another significant development enabling the “miniaturisation” of a protein array formed on a MALDI target derives from the application of the Applicant's COVET technology described in WO 01 / 57198. Briefly, using this technology they are able to create from cDNA libraries expressed proteins, which carry a “sequence tag” that can be used to capture the proteins with a high affinity and in a specific orientation on the microarray surface. This firstly enables proteins e.g. a protein library to be stably immobilized such that leaching of protein from the surface is avoided and secondly the oriented immobilisation of the fusion protein onto the surface ensure maximum biological activity

[0032] In this way the Applicant has been able to introduce the protein capture moieties not only in a homogeneous, spatial defined arrangement but also in a manner which enables high affinity binding in a specific manner. The resulting surface combines selectivity for the capture of biological macromolecules on the probe with reduced non specific binding of the type commonly observed on underivatised glass or metal surfaces and additionally results in a homogeneous distribution and orientation of the captured biological macromolecules.

[0034] In a preferred embodiment the probe has as it's protein capture moieties either a biotin binder e.g. neutravidin, avidin or streptavidin or a bleomycin resistant protein binder e.g. bleomycin. The proteins are bound to the probe to create a protein microarray by printing a plurality of bacterial, yeast, sf9 or mammalian cell lysates containing fusion proteins in which a high affinity tag e.g. biotin or zeocin resistant protein (ZRP) is expressed onto the capture surface. Proteins are derived from the expression of a cDNA library and each individual clone is tagged at the C-terminus and / or on the N-terminus with a consensus sequence, which will enable high affinity recognition of the protein even in the presence of the otherwise protein repellent molecules. Only the recombinant, tagged protein can recognise the capture surface and other proteins from the lysate can be washed away as they do not bind to the protein repellent surface and do not have a high affinity to the protein binding moieties present in the layer.

[0067] In contrast to the prior art in which matrix and analyte are co crystalised in an aqueous solvent, the Applicant uses two distinct steps in which first the protein is deposited in an aqueous solvent and then the energy absorbing molecules are deposited such that they crystallise out from the non aqueous solvent on the probe. This has the advantage that the protein is deposited in its biological form However, using a non aqueous solvent to deliver the energy absorbing molecules allows the formation of a homogenous layer of microcrystals. This has two benefits. First the formation of a homogenous layer means it is not necessary to search for a sweet spot as the homogenous layer guarantees protein in the presence of energy absorbing molecules and secondly it results in more accurate measurement due to the even nature of the layer.

Problems solved by technology

However, both methods suffer limitations due to their bias towards highly expressed proteins and the destructive method of separation.

The current methods of analysing protein microarrays are therefore restricted by the availability of appropriate labelled ligands.

However, for drug-like small molecules, which often have molecular weights of less than 1000 Da, neither radio- or fluorescent labels are desirable; radiolabels are disfavoured for health and safety reasons, whilst the introduction of a fluorophore into the small molecule could significantly perturb the structure activity profile in an unpredictable manner.

However, the development of a MALDI MS-compatible protein microarray is complex since existing methods for forming protein microarrays do not transfer readily onto to a MALDI target.

There are a number of reasons why this is the case, inter alia the specialised nature of the probe surfaces and the potential for salts present in reaction buffers to interfere with the detection method.

As a consequence it is often observed that individual crystals contain insufficient analyte for analysis by MALDI.

However, all these methods suffer from one or more of the following limitations: a) Partial or total loss of biological activity because of amine-based coupling of the analyte or the bait onto the probe; b) Low specificity between the analyte and the surface which can lead to the non-specific binding of several analytes to the surface (e.g. ion-exchange surfaces); c) Low affinity of the analyte to the surface which can lead to leaching of the analyte from the surface during any wash procedures (e.g. ion-exchange and nitriloacetic acid surfaces); d) The affinity capture surface lacks non specific protein resistance, which can lead to high levels of non-specific protein binding which would interfere with the analysis of a protein microarray, e) The availability of only a limited number of affinity capture proteins.

Thus existing methods do not enable the immobilisation of large numbers of different, purified proteins in the form of a MALDI MS-compatible microarray suitable for functional analysis of the microarrayed proteins.

Images