Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32304, USA.
Anal Bioanal Chem. 2023 Nov;415(27):6633-6645. doi: 10.1007/s00216-023-04957-4. Epub 2023 Sep 28.
Recent advances have rekindled the interest in ion mobility as an additional dimension of separation in mass spectrometry (MS)-based proteomics. Ion mobility separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ~4300 pairs of matching modified and unmodified peptide ion species by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.26%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between -1.4% (arginine citrullination) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM and is partially correlated with the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.
近年来，离子淌度作为质谱（MS）基蛋白质组学中分离的附加维度重新引起了人们的兴趣。离子淌度根据气相中离子的大小和形状对离子进行分离。在这里，我们着手研究 22 种不同的翻译后修饰（PTM）对肽的碰撞截面（CCS）的影响。我们总共通过被困离子淌度谱（TIMS）分析了~4300 对匹配的修饰和未修饰的肽离子对。基于掺入参考肽的线性对齐导致 CCS 值具有高度可重复性，中位数变异系数为 0.26%。在全局水平上，我们观察到在改变其电荷状态时，修饰肽的 m/z 与离子淌度空间之间重新分配。同一电荷状态下修饰肽与未修饰肽的成对比较显示 CCS 的中位数偏移在-1.4%（精氨酸瓜氨酸化）和+4.5%（O-GlcNAc 化）之间。一般来说，增加修饰肽的质量与更高的 CCS 值相关，特别是在同源 PTM 系列中。然而，更详细地研究离子群体，我们发现给定 PTM 的 CCS 变化可以有很大差异，并且部分与未修饰对应物的气相结构相关。总之，我们的研究表明 PTM 和序列特异性对肽的截面有影响，这可以进一步用于全蛋白质组 PTM 分析。
