Zhang Huoming, Bensaddek Dalila
Corelabs, King Abdullah University of Science and Technology, Thuwal 23500-6900, Kingdom of Saudi Arabia.
J Proteome Res. 2025 Feb 7;24(2):526-536. doi: 10.1021/acs.jproteome.4c00690. Epub 2025 Jan 22.
We introduce here a novel approach, termed time-segmented acquisition (Seg), to enhance the identification of peptides and proteins in trapped ion mobility spectrometry (TIMS)-time-of-flight (TOF) mass spectrometry. Our method exploits the positive correlation between ion mobility values and reversed-phase liquid chromatography (LC) retention time to improve ion separation and resolution. By dividing the LC retention time into multiple segments and applying a segment-specific narrower ion mobility range within the TIMS tunnel, we achieved better separation and higher resolution of ion mobility. In comparison to conventional TIMS methods, which typically scan a static ion mobility range (either from 0.6 to 1.6 [Wide] or from 0.85 to 1.3 [Narrow], V × s/cm), the Seg method demonstrates marked improvements in identification rates. Compared to Wide scanning, the Seg method increases peptide identifications by 17-27% and protein identifications by 6-16% depending on the gradient length and the sample load. The enhancement in peptide identification is even more pronounced when compared to Narrow scanning, with an increase of 34-86%. These findings highlight the potential of the Seg dda-PASEF method in expanding the capabilities of TIMS-TOF mass spectrometry, especially for peptide-focused analyses, such as post-translational modifications and peptidomics.
我们在此介绍一种名为时间分段采集（Seg）的新方法，以增强在捕集离子淌度质谱（TIMS）-飞行时间（TOF）质谱中对肽段和蛋白质的鉴定。我们的方法利用离子淌度值与反相液相色谱（LC）保留时间之间的正相关关系来改善离子分离和分辨率。通过将LC保留时间划分为多个段，并在TIMS通道内应用特定段的更窄离子淌度范围，我们实现了更好的离子淌度分离和更高的分辨率。与传统的TIMS方法相比，传统方法通常扫描一个静态的离子淌度范围（宽范围为0.6至1.6 [宽]或窄范围为0.85至1.3 [窄]，V×s/cm），Seg方法在鉴定率上有显著提高。与宽扫描相比，根据梯度长度和样品载量，Seg方法的肽段鉴定增加了17 - 27%，蛋白质鉴定增加了6 - 16%。与窄扫描相比，肽段鉴定的增强更为明显，增加了34 - 86%。这些发现突出了Seg dda - PASEF方法在扩展TIMS - TOF质谱功能方面的潜力，特别是对于聚焦肽段的分析，如翻译后修饰和肽组学。
