Pacific Northwest National Laboratory, Richland, WA 99352, USA.
BMC Bioinformatics. 2013 Feb 12;14:49. doi: 10.1186/1471-2105-14-49.
MultiAlign is a free software tool that aligns multiple liquid chromatography-mass spectrometry datasets to one another by clustering mass and chromatographic elution features across datasets. Applicable to both label-free proteomics and metabolomics comparative analyses, the software can be operated in several modes. For example, clustered features can be matched to a reference database to identify analytes, used to generate abundance profiles, linked to tandem mass spectra based on parent precursor masses, and culled for targeted liquid chromatography-tandem mass spectrometric analysis. MultiAlign is also capable of tandem mass spectral clustering to describe proteome structure and find similarity in subsequent sample runs.
MultiAlign was applied to two large proteomics datasets obtained from liquid chromatography-mass spectrometry analyses of environmental samples. Peptides in the datasets for a microbial community that had a known metagenome were identified by matching mass and elution time features to those in an established reference peptide database. Results compared favorably with those obtained using existing tools such as VIPER, but with the added benefit of being able to trace clusters of peptides across conditions to existing tandem mass spectra. MultiAlign was further applied to detect clusters across experimental samples derived from a reactor biomass community for which no metagenome was available. Several clusters were culled for further analysis to explore changes in the community structure. Lastly, MultiAlign was applied to liquid chromatography-mass spectrometry-based datasets obtained from a previously published study of wild type and mitochondrial fatty acid oxidation enzyme knockdown mutants of human hepatocarcinoma to demonstrate its utility for analyzing metabolomics datasets.
MultiAlign is an efficient software package for finding similar analytes across multiple liquid chromatography-mass spectrometry feature maps, as demonstrated here for both proteomics and metabolomics experiments. The software is particularly useful for proteomic studies where little or no genomic context is known, such as with environmental proteomics.
MultiAlign 是一款免费软件工具，通过跨数据集聚类质量和色谱洗脱特征，将多个液相色谱-质谱数据集彼此对齐。适用于无标记蛋白质组学和代谢组学比较分析，该软件可以以几种模式操作。例如，聚类特征可以与参考数据库匹配以识别分析物，用于生成丰度谱，基于母离子质量与串联质谱相关联，并用于靶向液相色谱-串联质谱分析。MultiAlign 还能够进行串联质谱聚类，以描述蛋白质组结构并在随后的样本运行中找到相似性。
MultiAlign 应用于从环境样本的液相色谱-质谱分析中获得的两个大型蛋白质组学数据集。通过将质量和洗脱时间特征与已建立的参考肽数据库中的特征进行匹配，鉴定出微生物群落数据集中已知宏基因组的肽。结果与 VIPER 等现有工具获得的结果相当，但具有能够追踪肽簇在现有串联质谱中的条件的附加优势。MultiAlign 进一步应用于从没有宏基因组的反应堆生物量群落的实验样本中检测跨实验样本的聚类。进一步分析了几个聚类以探索群落结构的变化。最后，MultiAlign 应用于先前发表的人类肝癌野生型和线粒体脂肪酸氧化酶敲低突变体的基于液相色谱-质谱的数据集，以证明其用于分析代谢组学数据集的效用。
MultiAlign 是一种在多个液相色谱-质谱特征图谱中查找相似分析物的有效软件包，如这里所示，适用于蛋白质组学和代谢组学实验。该软件对于蛋白质组学研究特别有用，在蛋白质组学研究中，基因组背景知之甚少，例如环境蛋白质组学。
