Artemenko Konstantin A, Zubarev Alexander R, Samgina Tatiana Yu, Lebedev Albert T, Savitski Mikhail M, Zubarev Roman A
Division of Molecular Biometry, Institute for Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Anal Chem. 2009 May 15;81(10):3738-45. doi: 10.1021/ac802532j.
A recent proteomics-grade (95%+ sequence reliability) high-throughput de novo sequencing method utilizes the benefits of high resolution, high mass accuracy, and the use of two complementary fragmentation techniques collision-activated dissociation (CAD) and electron capture dissociation (ECD). With this high-fidelity sequencing approach, hundreds of peptides can be sequenced de novo in a single LC-MS/MS experiment. The high productivity of the new analysis technique has revealed a new bottleneck which occurs in data representation. Here we suggest a new method of data analysis and visualization that presents a comprehensive picture of the peptide content including relative abundances and grouping into families. The 2D mass mapping consists of putting the molecular masses onto a two-dimensional bubble plot, with the relative monoisotopic mass defect and isotopic shift being the axes and with the bubble area proportional to the peptide abundance. Peptides belonging to the same family form a compact group on such a plot, so that the family identity can in many cases be determined from the molecular mass alone. The performance of the method is demonstrated on the high-throughput analysis of skin secretion from three frogs, Rana ridibunda, Rana arvalis, and Rana temporaria. Two dimensional mass maps simplify the task of global comparison between the species and make obvious the similarities and differences in the peptide contents that are obscure in traditional data presentation methods. Even biological activity of the peptide can sometimes be inferred from its position on the plot. Two dimensional mass mapping is a general method applicable to any complex mixture, peptide and nonpeptide alike.
一种最新的蛋白质组学级（序列可靠性达95%以上）高通量从头测序方法利用了高分辨率、高质量精度以及两种互补碎裂技术——碰撞诱导解离（CAD）和电子捕获解离（ECD）的优势。通过这种高保真测序方法，在单次液相色谱-串联质谱（LC-MS/MS）实验中可以对数百个肽段进行从头测序。这种新分析技术的高生产力揭示了数据呈现方面出现的一个新瓶颈。在此，我们提出一种新的数据分析和可视化方法，该方法能呈现肽段含量的全面情况，包括相对丰度以及分组归类。二维质量图谱是将分子质量绘制到二维气泡图上，以相对单同位素质量亏损和同位素位移为坐标轴，气泡面积与肽段丰度成正比。属于同一家族的肽段在这样的图谱上形成一个紧密的群组，这样在许多情况下仅从分子质量就能确定家族身份。该方法的性能在对三种青蛙（食用蛙、林蛙和欧洲林蛙）皮肤分泌物的高通量分析中得到了验证。二维质量图谱简化了物种间全局比较的任务，并使传统数据呈现方法中模糊不清的肽段含量的异同变得明显。甚至肽段的生物活性有时也能从其在图谱上的位置推断出来。二维质量图谱是一种适用于任何复杂混合物（无论是肽类还是非肽类）的通用方法。
