Two Dimensional Mass Spectrometry in a Linear Ion Trap

细胞、组织和有机体，包括人类，都是由包括蛋白质在内的各种分子组成的。蛋白质是“分子机器”，负责细胞的一切活动，从复制到处理营养物质。一个典型的细胞可能有由数以千计的蛋白质组成的10‘S，从事无数特定的化学“工作”，包括合成或回收其他蛋白质，因此蛋白质的组成是不断变化的。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。了解这些信息将使生物科学家，从基础研究人员到临床医生，更好地了解在营养不良、疾病、健康老龄化、干旱甚至药物治疗的条件下细胞内发生的事情。开发更好的方法来准确和足够详细地测量蛋白质组是支持研究目标的关键，这将导致更好的科学、更好的技术，并最终带来更好的健康和更健康的食品。我们最近在一项名为二维质谱的新技术上取得了实质性进展，该技术提供了对样本中的所有肽/蛋白质组分进行排序的能力，而不是选择几个。我们已经在几个出版物和整个蛋白质组分析的初步数据中展示了这项技术的工作。此外，我们还通过离子轨迹模拟证明，这种二维质谱学方法并不一定局限于FTICR质谱仪，还可以适用于成本较低的线性离子陷阱质谱仪。然而，在实现这一愿景之前，我们必须应对一些特殊的挑战。这项提议旨在解决这些挑战。首先，我们已经建立了一个原型仪器，但我们必须对其进行优化、调整和测试蛋白质组样本。其次，我们需要实际获取这些蛋白质组样本的数据，使用一些标准，如酵母细胞。第三，我们的目标是探索可能允许进行三维质谱学实验的新方法。第四，我们需要调整来自这台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出使用这一令人兴奋的新技术进行最佳蛋白质组分析的协议和方法，以及使用更小、更便宜的质谱仪生成用于提取整个细胞和组织的蛋白质序列信息的二维质谱学数据的能力。

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.