Two Dimensional Mass Spectrometry in a Linear Ion Trap

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Cells, tissues, and organisms, including humans, are made of a variety of molecules, including proteins. Proteins are the 'molecular machines' responsible for everything a cell does, from replication to processing nutrients. A typical cell might have 10's of thousands of proteins doing myriad particular chemical 'jobs', including synthesizing or recycling other proteins, so the complement of proteins is constantly changing. The field of proteomics involves detecting as many of these proteins as possible, understanding how they change with time and in reaction to stress or chemical treatment. Knowing this information will allow bioscientists, from basic researchers to clinicians, to better understand what is occurring in the cell under conditions of malnutrition, disease, healthy aging, drought, or even pharmaceutical treatment. Developing better methods to measure the 'proteome' accurately and with sufficient detail is a key underpinning research goal which results in better science, better technology, and ultimately better health and healthier food. We have recently made substantial advances in a novel technology, called 2-dimensional mass spectrometry, which offers the capability to sequence all peptide/protein components in a sample, rather than a select few. We have demonstrated the technology works in several publications and in preliminary data on a whole proteomic analysis herein. Additionally, we have demonstrated by ion trajectory modelling, that this 2-dimensional mass spectrometry method is not necessarily limited to the FTICR mass spectrometers, but can also be adapted to the less costly linear ion trap mass spectrometers. However, there are some particular challenges which we must address before the vision can be attained. This proposal aims to solve those challenges.Firstly, we have built a prototype instrument but we must optimise, tune, and test it for proteomic samples. Secondly, we need to actually acquire data on those proteomic samples, using some standards such as yeast cells. Thirdly, we aim to explore new methodologies that might allow 3-dimensional mass spectrometry experiments. And, fourthly, we need to adapt the data from this 2DMS-LIT instrument to our data processing algorithms already in place. The overall result of this project will be the development of protocols and methods for optimal proteomic analysis using this exciting new technology and the ability to generate 2-dimensional mass spectrometry data for extraction of protein sequence information for whole cells and tissues, using a smaller, cheaper mass spectrometer.