Jaitly Navdeep, Monroe Matthew E, Petyuk Vladislav A, Clauss Therese R W, Adkins Joshua N, Smith Richard D
Environmental Molecular Science Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
Anal Chem. 2006 Nov 1;78(21):7397-409. doi: 10.1021/ac052197p.
Liquid chromatography coupled to mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS/MS) has become a standard technique for analyzing complex peptide mixtures to determine composition and relative abundance. Several high-throughput proteomics techniques attempt to combine complementary results from multiple LC-MS and LC-MS/MS analyses to provide more comprehensive and accurate results. To effectively collate and use results from these techniques, variations in mass and elution time measurements between related analyses need to be corrected using algorithms designed to align the various types of data: LC-MS/MS versus LC-MS/MS, LC-MS versus LC-MS/MS, and LC-MS versus LC-MS. Described herein are new algorithms referred to collectively as liquid chromatography-based mass spectrometric warping and alignment of retention times of peptides (LCMSWARP), which use a dynamic elution time warping approach similar to traditional algorithms that correct for variations in LC elution times using piecewise linear functions. LCMSWARP is compared to the equivalent approach based upon linear transformation of elution times. LCMSWARP additionally corrects for temporal drift in mass measurement accuracies. We also describe the alignment of LC-MS results and demonstrate their application to the alignment of analyses from different chromatographic systems, showing the suitability of the present approach for more complex transformations.
液相色谱-质谱联用（LC-MS）和串联质谱联用（LC-MS/MS）已成为分析复杂肽混合物以确定其组成和相对丰度的标准技术。几种高通量蛋白质组学技术试图将来自多个LC-MS和LC-MS/MS分析的互补结果相结合，以提供更全面、准确的结果。为了有效地整理和使用这些技术的结果，需要使用旨在对齐各种类型数据的算法来校正相关分析之间质量和洗脱时间测量的差异：LC-MS/MS与LC-MS/MS、LC-MS与LC-MS/MS以及LC-MS与LC-MS。本文描述了一种统称为基于液相色谱的质谱峰展宽和肽保留时间对齐（LCMSWARP）的新算法，该算法使用类似于传统算法的动态洗脱时间峰展宽方法，传统算法使用分段线性函数校正LC洗脱时间的差异。将LCMSWARP与基于洗脱时间线性变换的等效方法进行了比较。LCMSWARP还校正了质量测量精度的时间漂移。我们还描述了LC-MS结果的对齐，并展示了它们在不同色谱系统分析对齐中的应用，表明本方法适用于更复杂的变换。
