NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data

Abstract

Summary: Most current stable isotope-based methodologies are targeted and focus only on the well-described aspects of metabolic networks. Here, we present NTFD (non-targeted tracer fate detection), a software for the non-targeted analysis of all detectable compounds derived from a stable isotope-labeled tracer present in a GC/MS dataset. In contrast to traditional metabolic flux analysis approaches, NTFD does not depend on any a priori knowledge or library information. To obtain dynamic information on metabolic pathway activity, NTFD determines mass isotopomer distributions for all detected and labeled compounds. These data provide information on relative fluxes in a metabolic network. The graphical user interface allows users to import GC/MS data in netCDF format and export all information into a tab-separated format.Availability: NTFD is C++- and Qt4-based, and it is freely available under an open-source license. Pre-compiled packages for the installation on Debian- and Redhat-based Linux distributions, as well as Windows operating systems, along with example data, are provided for download at http://ntfd.mit.edu/.Contact: gregstep@mit.edu

Non-targeted Tracer Fate Detection

“…Isomers that differ only in their isotopic composition with otherwise identical structure, including isotopic substitutions of different elements [22]. For example [U- 13 C]acetate ([1,2-13 C 2 ]acetate), [1-13 C]acetate, and [2,2,2-D 3 ]acetate are isotopologic. In carbon labeling experiments, the term is often implicitly used to only refer to 13 C-isotopologues.…”

“…Mass isotopomers are referred to as M i , M i, or M +i, where i indicates the increase in nominal mass as compared to the lightest isotopologue. For example, for carbon labeling of acetate, M 1 comprises [1- 13 C]acetate and [2-13 C]acetate.…”

“…For example, [1- 13 MID The mass isotopomer distribution (MID) is the relative abundance of the different mass isotopomers of a molecule. MIDs can be determined from mass spectrometric measurements and are often the basis for 13 C-MFA, a method for metabolic flux analysis based on stable isotope labeling and stoichiometric modeling, where a set of fluxes through a predefined metabolic network is determined that can best explain the experimentally observed isotopic labeling.…”

“…Although many metabolic pathways are well described and known since many years, new reactions are continuously being identified, [10,11] underlining the necessity for a global detection of isotopic enrichment. Recently, several tools for the non-targeted detection of isotopic enrichment in mass spectrometric data have been developed [12][13][14][15][16][17][18].…”

“…Unlike conventional mass spectrometric methods, IRMS cannot be used to determine MIDs. However, MIDs can provide interesting insights into metabolism and are the basis for 13 C-metabolic flux analysis ( 13 C-MFA) [20,21].…”