Two Dimensional Mass Spectrometry in a Linear Ion Trap

细胞，组织和生物体，包括人类，是由各种分子组成的，包括蛋白质。蛋白质是“分子机器”，负责细胞所做的一切，从复制到处理营养物质。一个典型的细胞可能有成千上万的蛋白质做无数特定的化学“工作”，包括合成或回收其他蛋白质，所以蛋白质的补充是不断变化的。蛋白质组学领域涉及检测尽可能多的这些蛋白质，了解它们如何随时间变化以及对压力或化学处理的反应。了解这些信息将使从基础研究人员到临床医生的生物科学家能够更好地了解在营养不良，疾病，健康衰老，干旱甚至药物治疗的条件下细胞中发生的事情。开发更好的方法来准确和足够详细地测量“蛋白质组”是一个关键的基础研究目标，这将导致更好的科学，更好的技术，最终更好的健康和更健康的食品。我们最近在一项称为二维质谱的新技术方面取得了重大进展，该技术能够对样品中的所有肽/蛋白质组分进行测序，而不是选择少数几种。我们已经在几个出版物和本文中的整个蛋白质组学分析的初步数据中证明了该技术的工作。此外，我们已经通过离子轨迹建模证明，这种二维质谱法不一定限于FTICR质谱仪，但也可以适用于成本较低的线性离子阱质谱仪。然而，在实现这一愿景之前，我们必须应对一些特殊挑战。该提案旨在解决这些挑战。首先，我们已经建立了一个原型仪器，但我们必须优化，调整和测试它的蛋白质组样本。其次，我们需要使用一些标准品（如酵母细胞）实际获取这些蛋白质组样本的数据。第三，我们的目标是探索新的方法，可能允许三维质谱实验。而且，我们需要调整来自这个2DMS-LIT仪器的数据，以适应我们已经到位的数据处理算法。该项目的总体结果将是开发使用这种令人兴奋的新技术进行最佳蛋白质组学分析的协议和方法，以及使用更小，更便宜的质谱仪生成二维质谱数据以提取整个细胞和组织的蛋白质序列信息的能力。

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.