组蛋白序列中的氨基酸位置和翻译后修饰 (PTM) 的化学性质对于阐明“组蛋白密码”至关重要。先前的工作表明，PTM 会诱导特定的生物反应，并且是作为诊断生物标志物的良好候选者。在这里，我们评估了俘获离子淌度 (TIMS) 与并行累积-串行碎片 (PASEF) 和串联质谱 (MS/MS) 对模型癌细胞自下而上蛋白质组学的分析优势。该研究还考虑了纳米液体色谱 (LC) 和传统方法的使用：LC-TIMS-PASEF-ToF MS/MS 与 nLC-TIMS-PASEF-ToF MS/MS 与 nLC-MS/MS。由于增加了分离尺寸，TIMS 和 PASEF-MS/MS 的添加增加了检测到的肽的数量。所有三种方法均在 MS 域中表现出高重现性和低 RSD (<5 ppm)。虽然 LC、nLC 和 TIMS 分离显示样品间的 RSD 较小，但准确的迁移率 (1/K0) 测量（<0.6% RSD）提高了肽分配的置信度。观察到有关 PTM（例如 ac、me1-3）及其相应未修饰丙酰化肽（有助于肽分配）的数量和类型的保留时间和迁移率趋势。迁移率分离允许对共洗脱结构和位置异构体进行注释，并且与 nLC-MS/MS 相比，由于减少了化学噪音而显示出多种优势。

The amino acid position within a histone sequence and the chemical nature of post-translational modifications (PTMs) are essential for elucidating the "Histone Code". Previous work has shown that PTMs induce specific biological responses and are good candidates as biomarkers for diagnostics. Here, we evaluate the analytical advantages of trapped ion mobility (TIMS) with parallel accumulation-serial fragmentation (PASEF) and tandem mass spectrometry (MS/MS) for bottom-up proteomics of model cancer cells. The study also considered the use of nanoliquid chromatography (LC) and traditional methods: LC-TIMS-PASEF-ToF MS/MS vs nLC-TIMS-PASEF-ToF MS/MS vs nLC-MS/MS. The addition of TIMS and PASEF-MS/MS increased the number of detected peptides due to the added separation dimension. All three methods showed high reproducibility and low RSD in the MS domain (<5 ppm). While the LC, nLC and TIMS separations showed small RSD across samples, the accurate mobility (1/K0) measurements (<0.6% RSD) increased the confidence of peptide assignments. Trends were observed in the retention time and mobility concerning the number and type of PTMs (e.g., ac, me1-3) and their corresponding unmodified, propionylated peptide that aided in peptide assignment. Mobility separation permitted the annotation of coeluting structural and positional isomers and compared with nLC-MS/MS showed several advantages due to reduced chemical noise.