LC-MS/MS pipeline: an Excel based interface for the study of LC-MS data from the metabolomics environment

Abstract

The area of metabolomics has broadened over the last decade with growing popularity in numerous applications. Nonetheless, ultimate challenges still persist in both interpreting and gathering metabolomics data. To date there is no such interface, software or online tool that can accomplish all the analysis for metabolite identification of LC-MS data in a single package. In response to overcome these challenges, I have made an interface that makes use of the available popular online web-based tools in the area of the metabolomics environment. The interface that I made is called the LC-MS/MS Pipeline which is an Excel based Interface for the analysis of LCMS data. The pipeline utilizes all the existing accessible online tools like METLIN database (http://metlin.scripps.edu/), MetaboAnalyst (http://metaboanalyst.ca/), MetFusion (http://msbi.ipbhalle. de/MetFusion/), MetFrag (http://msbi.ipb-halle.de/MetFrag/) and MassBank (http://www.massbank.jp/) for the study of LC-MS data. Considering, the study of LC-MS data being a huge approach, the pipeline that I have made comprises four modules which are “MSMS and Annotated Compounds Only”, “MSMS and Non-Annotated Compounds Only”, “Non-MSMS and Annotated Compounds Only” and lastly, “Non-MSMS and Non-Annotated Compounds Only”. In each module, there are 8 steps for the analysis of LC-MS data except the first module (MSMS and Annotated Compounds Only) which has 9 steps. The first and second steps in the approach of the LCMS/ MS Pipeline are the processes of Ion Annotation and Ion Annotation Result respectively. The process of Ion Annotation utilizes the package of CAMERA, available from Bioconductor (http://bioconductor.org/) and the METLIN database to generate its results. The third step is the process of Mass-Based Search Result which utilizes the outcomes generated from the process of Ion Annotation to produce its results. The fourth and the fifth steps in the approach of the LC-MS/MS Pipeline is the process of multivariate analysis which is divided into two steps. Step-1 generates the peak intensity/stats table that can then be utilized to perform statistical/multivariate analysis of LC-MS data though MetaboAnalyst in step-2. The sixth, seventh and eight steps in the LC-MS/MS Pipeline involve the process of pathway analysis by compound name, the process of pathway analysis by KEGG ID, and the process of enrichment analysis by compound name. The processes are utilized for the pathway and enrichment analysis of LC-MS data through MetaboAnalyst. The ninth step which is available to the “MSMS and annotated Compounds Only” module is the process of Full Tandem MSMS Analysis, which is utilized for the tandem MSMS analysis of LC-MS data through MetFusion. All of the above mentioned processes for the pipeline are carried out with the help of web automation. Although the pipeline that I made utilizes the assistance of the online based tools to generate its results and does not have any database or repository of its own, still it can achieve all the required analysis for the LC-MS data with a just click of a button and, moreover, is user-friendly.