Additional file 1 of Bridging the gap between non-targeted stable isotope labeling and metabolic flux analysis

Supplemental information. List of isotopically enriched compounds and their mass isotopomer distributions; selected mass spectra. (PDF 308 kb

Fragment Formula Calculator (FFC): Determination of Chemical Formulas for Fragment Ions in Mass Spectrometric Data

The accurate determination of mass isotopomer distributions (MID) is of great significance for stable isotope-labeling experiments. Most commonly, MIDs are derived from gas chromatography/electron ionization mass spectrometry (GC/EI-MS) measurements. The analysis of fragment ions formed during EI, which contain only specific parts of the original molecule can provide valuable information on the positional distribution of the label. The chemical formula of a fragment ion is usually applied to derive the correction matrix for accurate MID calculation. Hence, the correct assignment of chemical formulas to fragment ions is of crucial importance for correct MIDs. Moreover, the positional distribution of stable isotopes within a fragment ion is of high interest for stable isotope-assisted metabolomics techniques. For example, ¹³C-metabolic flux analyses (¹³C-MFA) are dependent on the exact knowledge of the number and position of retained carbon atoms of the unfragmented molecule. Fragment ions containing different carbon atoms are of special interest, since they can carry different flux information. However, the process of mass spectral fragmentation is complex, and identifying the substructures and chemical formulas for these fragment ions is nontrivial. For that reason, we developed an algorithm, based on a systematic bond cleavage, to determine chemical formulas and retained atoms for EI derived fragment ions. Here, we present the fragment formula calculator (FFC) algorithm that can calculate chemical formulas for fragment ions where the chemical bonding (e.g., Lewis structures) of the intact molecule is known. The proposed algorithm is able to cope with general molecular rearrangement reactions occurring during EI in GC/MS measurements. The FFC algorithm is able to integrate stable isotope labeling experiments into the analysis and can automatically exclude candidate formulas that do not fit the observed labeling patterns. We applied the FFC algorithm to create a fragment ion repository that contains the chemical formulas and retained carbon atoms of a wide range of trimethylsilyl and <i>tert</i>-butyldimethylsilyl derivatized compounds. In total, we report the chemical formulas and backbone carbon compositions for 160 fragment ions of 43 alkylsilyl-derivatives of primary metabolites. Finally, we implemented the FFC algorithm in an easy-to-use graphical user interface and made it publicly available at http://www.ffc.lu

Methodological detection solution scaffolds response to mechanical stress, depending on the degree of hydration

Title: Methodological detection solution scaffolds response to mechanical stress, depending on the degree of hydration Objectives: Determining the extent of lateral deformation u scaffolds made of PVA polymer electrospinning technique. Identify the extent of differences in transverse deformation for different groups of nanofiber scaffolds made of PVA polymer electrospinning technique. Methods: Research scaffolds, we used a measuring device μ-tester, which has two jaws. For the measurement, we chose uniaxial tension test in -tester and record the fluorescence microscope was used with HD camera Olympus 320 for online video recording. Results: The results of this study showed that the ratio of the samples U: L and crosslinking time affects the degree of lateral deformation of the samples scaffolds. Samples scaffolds are compressible, some groups even reached the limits of incompressibility 0.5 Poisson's ratio. Keywords: Poisson, Poisson's ratio, scaffold, nanofiber scaffold, scaffold hydrated, electrospun scaffold, lateral deformatio

Additional file 5 of The role of HIF-1 in oncostatin M-dependent metabolic reprogramming of hepatic cells

Table S3. Mass isotopomer distributions (MIDs) from [13C5]glutamine in PH5CH8 immortalized human hepatocytes treated for 36 h with 50 ng/mL OSM or left untreated. MIDs were corrected for natural isotope abundance. (PDF 94.2 kb