Ultrafast Peptide Label-Free Quantification with FlashLFQ,Journal of Proteome Research

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Ultrafast Peptide Label-Free Quantification with FlashLFQ
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2017-11-08 00:00:00 , DOI: 10.1021/acs.jproteome.7b00608
Robert J. Millikin ₁ , Stefan K. Solntsev ₁ , Michael R. Shortreed ₁ , Lloyd M. Smith _{1,

2}

Affiliation

The rapid and accurate quantification of peptides is a critical element of modern proteomics that has become increasingly challenging as proteomic data sets grow in size and complexity. We present here FlashLFQ, a computer program for high-speed label-free quantification of peptides following a search of bottom-up mass spectrometry data. FlashLFQ is approximately an order of magnitude faster than established label-free quantification methods. The increased speed makes it practical to base quantification upon all of the charge states for a given peptide rather than solely upon the charge state that was selected for MS2 fragmentation. This increases the number of quantified peptides, improves replicate-to-replicate reproducibility, and increases quantitative accuracy. We integrated FlashLFQ into the graphical user interface of the MetaMorpheus search software, allowing it to work together with the global post-translational modification discovery (G-PTM-D) engine to accurately quantify modified peptides. FlashLFQ is also available as a NuGet package, facilitating its integration into other software, and as a standalone command line software program for the quantification of search results from other programs (e.g., MaxQuant).

中文翻译：

利用FlashLFQ进行超快肽段无标签定量

肽段的快速，准确定量是现代蛋白质组学的关键要素，随着蛋白质组学数据集的规模和复杂性的增长，这一挑战变得日益严峻。我们在这里介绍FlashLFQ，这是一种自下而上质谱数据搜索之后用于肽段的高速无标签定量的计算机程序。与已建立的无标记定量方法相比，FlashLFQ大约快一个数量级。提高的速度使基于给定肽的所有电荷状态的定量而不是仅基于为MS2片段化选择的电荷状态的定量成为可能。这增加了定量肽的数量，提高了复制之间的可重复性，并提高了定量准确性。我们将FlashLFQ集成到MetaMorpheus搜索软件的图形用户界面中，使其可以与全球翻译后修饰发现（G-PTM-D）引擎一起使用，以准确地定量修饰的肽。FlashLFQ还可以作为NuGet软件包使用，以促进其与其他软件的集成，也可以作为独立的命令行软件程序来量化其他程序（例如MaxQuant）的搜索结果。

更新日期：2017-11-09

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