随着人们越来越认识和认识到蛋白质组的真正复杂性,我们终于进入了后蛋白质组学时代.将蛋白质组常规评估为基因序列的推断相关性(即,典型的“蛋白质”)不能提供必要的系统级生物学关键分析,需要了解潜在的分子机制和途径或确定最具选择性的生物标志物和治疗靶标。这些关键要求需要在蛋白质形式/蛋白质种类的水平上分析蛋白质组,实际活跃的分子玩家。目前,只有高度精细的整合或整合的自上而下的蛋白质组学(iTDP)才能提供必要的分析深度,全面,以及对天然系统固有的最广泛蛋白质形式的定量蛋白质组评估。在这里,我们提供了一个广阔的视野,结合历史和当前现实,为了建立对该领域来自何处的更平衡的理解(特别是在Proteome推出以来的十年中),当前问题,以及如果有必要,深度蛋白质组分析要成功,事情可能需要如何进行。我们基于我们的坚定信念,最好的蛋白质组学分析反映,尽可能接近,采样时的本地样本。我们还试图强调,这种和未来的分析方法可能最好基于对当前成功方法的互补性的广泛认识和利用。这也强调需要不断评估和进一步优化既定的方法,为了避免思想和期望的自满,也为了促进批判性和谨慎的发展和新方法的引入,最值得注意的是那些解决蛋白质的。最重要的是,我们希望强调,对分析质量的严格关注必须超越当前的思维,这种思维在很大程度上重视分析速度;后者肯定会很好,如果只有蛋白形式可以有效地,常规,并定量评估。唉,蛋白质组由蛋白质组成,不是可以扩增或直接反映基因的分子物种(即,\'规范\')。这个问题很难,我们必须接受并解决它,但是在进行这种更长时间的严格的深度蛋白质组分析游戏中的回报是更多选择性生物标志物的承诺,药物靶标,真正个性化甚至个性化的医疗。
With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical \'proteins\') cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of
proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of
proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address
proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only
proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of
proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., \'canonical\'). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine.