Download Metabolomics Workflow Guide

Before You Begin
Required items
• AMDIS
AMDIS is an acronym for the automated mass spectral deconvolution and identification system developed by NIST. (http://www.amdis.net) AMDIS helps analyze
GC-MS data of complex mixtures, even data with strong background ions and
coeluting peaks. AMDIS is not for use with data collected in SIM mode. AMDIS
automatically extracts pure (background free) component mass spectra from
highly complex GC-MS data files and uses these purified spectra when searching
a mass spectral library.
• MassHunter ID Browser B.03.01 or later
ID Browser, which is built into Mass Profiler Professional and Qualitative Analysis, performs compound identification using:
• LC/MS Personal Compound Database (METLIN, pesticides, forensics)
• GC/MS libraries (NIST and Fiehn library)
• Empirical Formula Calculation using Agilent's Molecular Formula Generator
(MFG) algorithm
Compounds may be quickly and easily identified within the Mass Profiler Professional environment. ID Browser automatically annotates the entity list and puts
the compound names onto any of the various visualization and pathway analysis
tools.
• METLIN Personal Compound Database and Library
METLIN personal compound database and library (PCDL) contains over 25,000
compounds, including 8,000 lipids with retention times for about 700 standards.
Used with TOF and Q-TOF data, identification is enabled using accurate mass
and/or retention time database searching. Searching the MS/MS spectral library
with more than 2,200 compounds enables more confident identification. PCDL
represents a data management system designed to assist in a broad array of
metabolite research and metabolite identification by providing public access to its
repository of current and comprehensive mass spectral metabolite data.
(http://metlin.scripps.edu/)
• Agilent Fiehn GC/MS Metabolomics Library
The Agilent Fiehn GC/MS Metabolomics RTL Library, developed in cooperation
with Dr. Oliver Fiehn, is a growing metabolomics-specific library that contains
searchable EI spectra and retention-time indexes for approximately 700 common
metabolites. The Fiehn library integrates with Agilent's other software tools for
GC/MS metabolomics to deliver metabolite identities faster and expand knowledge of metabolomic samples.
11