Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification.,Journal of Proteome Research

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Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification.
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2020-09-07 , DOI: 10.1021/acs.jproteome.0c00209
Sung-Huan Yu ₁ , Pelagia Kyriakidou ₁ , Jürgen Cox _{1,

2}

Affiliation

Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here, we introduce two novel algorithms implemented in MaxQuant that substantially improve the data analysis with multiple n-plexes. First, isobaric matching between runs makes use of the three-dimensional MS1 features to transfer identifications from identified to unidentified MS/MS spectra between liquid chromatography–mass spectrometry runs in order to utilize reporter ion intensities in unidentified spectra for quantification. On typical datasets, we observe a significant gain in MS/MS spectra that can be used for quantification. Second, we introduce a novel PSM-level normalization, applicable to data with and without the common reference channel. It is a weighted median-based method, in which the weights reflect the number of ions that were used for fragmentation. On a typical dataset, we observe complete removal of batch effects and dominance of the biological sample grouping after normalization. Furthermore, we provide many novel processing and normalization options in Perseus, the companion software for the downstream analysis of quantitative proteomics results. All novel tools and algorithms are available with the regular MaxQuant and Perseus releases, which are downloadable at http://maxquant.org.

中文翻译：

MaxQuant中运行之间的等压匹配和新颖的PSM级归一化极大地改善了基于报告子离子的定量。

等压标记有望将高样品多路复用与精确定量相结合。然而，正常化问题以及完整的缺失值问题ň -plexes跨多个篮子量化ñ -plex。在这里，我们介绍了在MaxQuant中实现的两种新颖算法，这些算法可显着改善多个n值的数据分析-丛。首先，运行之间的等压匹配利用三维MS1功能在液相色谱-质谱分析运行之间将标识从已识别的MS / MS谱转移到未识别的MS / MS谱，以便利用未识别谱中的报告离子强度进行定量。在典型的数据集上，我们观察到了可用于定量的MS / MS光谱的显着提高。其次，我们介绍了一种新颖的PSM级规范化，适用于有和没有公共参考通道的数据。这是一种基于中值的加权方法，其中的权重反映了用于碎片化的离子数。在典型的数据集上，我们观察到归一化后批次效应的完全消除和生物样品分组的优势。此外，我们在Perseus（用于定量蛋白质组学结果的下游分析的配套软件）中提供了许多新颖的处理和标准化选项。MaxQuant和Perseus的常规发行版提供了所有新颖的工具和算法，可从http://maxquant.org下载。

更新日期：2020-10-02

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