Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
Bruker Daltonik GmbH, Farenheitstr. 4, 28359 Bremen, Germany.
Mol Cell Proteomics. 2020 Jun;19(6):1058-1069. doi: 10.1074/mcp.TIR119.001720. Epub 2020 Mar 10.
Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. Required for this is suitable software that extracts the information contained in the four-dimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides and proteins in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org.
离子淌度可在基于 LC-MS 的鸟枪法蛋白质组学中增加一个维度，从而有可能提高蛋白质组覆盖率、定量准确性和动态范围。这需要合适的软件，该软件可提取由质荷比 (m/z)、保留时间、离子淌度和信号强度构成的四维 (4D) 数据空间中包含的信息。本文描述了离子淌度增强型 MaxQuant 软件，该软件利用了增加的数据维度。它提供了一个端到端的计算工作流程，用于鉴定和定量 LC-IMS-MS/MS 鸟枪法蛋白质组学数据中的肽和蛋白质。我们将其应用于与四极杆飞行时间 (QTOF) 分析仪联用的俘获离子淌度谱 (TIMS)。高度并行的 4D 特征检测算法可提取峰，然后将其组装成同位素图案。质量使用基于样本中肽的非线性 m/z、保留时间、离子淌度和信号强度相关模型进行重新校准。新的跨运行匹配 (MBR) 算法在匹配过程中利用 MS1 特征的碰撞截面 (CCS) 值，从额外维度显著提高了特异性。在 MBR 中使用 CCS 值的前提是在运行之间对离子淌度值进行相对对齐。CCS 感知的 MBR 极大地减少了在许多样本中进行蛋白质定量时的缺失值问题。还实现了 MS1 水平无标记定量，在具有已知真实值的基准数据集上证明具有高度的精确性和准确性。LC-IMS-MS/MS 的 MaxQuant 是基本 MaxQuant 版本的一部分，可从 http://maxquant.org 下载。
