User Manual for FT-MS

   User Manual for TOF-MS

   How to Cite


  • IsoMS is used to process chemical isotope labeling LC-MS data. The overall workflow includes the following three steps:

    Step 1: Convert the raw LC-MS data into a centroid peak list file* and store all the files in a folder;

    Step 2: Use the IsoMS script to process all the files;

    Step 3: Use the IsoMS-align script to align the peak pairs and their ratios from the datasets generated in Step 2 to produce a final CSV file that can be exported for data and statistics analysis. * Data conversion is done by using a built-in software from the MS manufacturer. The instruction(and a script for Bruker data) can be downloaded here (for Bruker FT-MS and TOF-MS data, download BD-convert; for Agilent TOF data, download AG-convert; for Waters TOF data, download WA-convert).

  • The current version of IsoMS consists of two scripts written in R (Windows). One is for peak picking, peak pairing and peak ratio calculation (download either IsoMS for TOF-MS or IsoMS for FT-MS) and another one is for alignment of peak pairs and their peak ratios from multiple LC-MS datasets (download IsoMS-align). All the scripts can be freely downloaded for non-commercial use.

  • The User Manual (download the PDF file for FT-MS and TOF-MS ) provides the instructions on the use of these two scripts for processing the chemical isotope labeling MS data to generate quantitative results in CSV file format that can be exported for further data and statistics analysis.