Comparison Log
2024-06-09 06:19:00.180540
mwtab Python Library Version: 1.2.5
Source:      https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN004666/mwtab/...
Study ID:    ST002848
Analysis ID: AN004666
Status:      Inconsistent

Sections "SAMPLEPREP" contain missmatched items: {('SAMPLEPREP_SUMMARY', "Lipid extraction. CD1 and MHC proteins were extracted in chloroform: methanol: water (2:2:1) (V: V: V) (Figure S1) at room temperature for 30 mins and centrifuged at 500g for 10 mins. The aqueous phase contained few lipids, so the combined interphase and organic phase were transferred and stored at -20°C for comparative lipidomics analysis, which was conducted in parallel with groups of lipid extracts. Mass spectrometry-based comparative lipidomics. Lipid eluents were annormalized to protein mass (20-80 μg), dried under nitrogen at 20°C, dissolved and briefly sonicated in starting mobile phase, which was 100% solvent B containing 70% hexanes, 30% isopropanol, 0.1% formic acid, and 0.05% ammonium hydroxide. Triplicate samples for each protein analyzed with blanks that were intermixed and monitored for lipid carryover, using an Agilent 1200 series HPLC autosampler with an Agilent 6520 Accurate-Mass Q-TOF MS controlled by MassHunter software. A normal phase gradient with solvent A (70% isopropanol, 30% methanol, 0.1% formic acid, and 0.05% ammonium hydroxide) and solvent B through a MonoChrom Diol column (3 μm X 150 mm X 2 mm; Varian, A0542150X020) were connected to a MetaGuard guard column (2 mm, Varian, A0542-MG2). The binary gradient was monitored with solvent B with 100% at 0-10 min, 50% at 17-22 min, 0% at 30-35 min, and 100% at 40-50 min, followed by an additional 0% for 6 min post-run for regeneration. Ionization occurred with a dual-electrospray ionization source maintained at 325°C with a drying gas flow of 5 L/min, nebulizer pressure of 30 pounds per square inch, and a capillary voltage of 5.5 kV. Positive- and negative-ion modes were typically monitored between m/z 100-3000 with the acquisition rate of 1.4 spectra/sec and 713.7 ms/spectrum. Internal calibrants (Agilent G1969-85001, m/z 121.050573, 922.009798) were continuously monitored to assess electrospray efficiency and mass accuracy. NanoESI-CID-MS was typically performed at a collision energy of 35V and an isolation width of 1.3 m/z and adjusted to optimize signal during individual experiments. For the semi-quantitative analysis of PCs and SMs eluted from cleavable CD1, the lipid eluents were normalized based on input protein and 10 µl were injected into a reverse-phase HPLC-MS system (Agilent Poroshell EC-C18 column, 1.9-micron, 3 x 50 mm with an Agilent 6520 QTOF mass spectrometry).(van ''t Klooster et al., 2020)"), ('SAMPLEPREP_SUMMARY', "Lipid extraction. CD1 and MHC proteins were extracted in chloroform: methanol: water (2:2:1) (V: V: V) (Figure S1) at room temperature for 30 mins and centrifuged at 500g for 10 mins. The aqueous phase contained few lipids, so the combined interphase and organic phase were transferred and stored at -20°C for comparative lipidomics analysis, which was conducted in parallel with groups of lipid extracts. Mass spectrometry-based comparative lipidomics. Lipid eluents were annormalized to protein mass (20-80 μg), dried under nitrogen at 20°C, dissolved and briefly sonicated in starting mobile phase, which was 100% solvent B containing 70% hexanes, 30% isopropanol, 0.1% formic acid, and 0.05% ammonium hydroxide. Triplicate samples for each protein analyzed with blanks that were intermixed and monitored for lipid carryover, using an Agilent 1200 series HPLC autosampler with an Agilent 6520 Accurate-Mass Q-TOF MS controlled by MassHunter software. A normal phase gradient with solvent A (70% isopropanol, 30% methanol, 0.1% formic acid, and 0.05% ammonium hydroxide) and solvent B through a MonoChrom Diol column (3 μm X 150 mm X 2 mm; Varian, A0542150X020) were connected to a MetaGuard guard column (2 mm, Varian, A0542-MG2). The binary gradient was monitored with solvent B with 100% at 0-10 min, 50% at 17-22 min, 0% at 30-35 min, and 100% at 40-50 min, followed by an additional 0% for 6 min post-run for regeneration. Ionization occurred with a dual-electrospray ionization source maintained at 325°C with a drying gas flow of 5 L/min, nebulizer pressure of 30 pounds per square inch, and a capillary voltage of 5.5 kV. Positive- and negative-ion modes were typically monitored between m/z 100-3000 with the acquisition rate of 1.4 spectra/sec and 713.7 ms/spectrum. Internal calibrants (Agilent G1969-85001, m/z 121.050573, 922.009798) were continuously monitored to assess electrospray efficiency and mass accuracy. NanoESI-CID-MS was typically performed at a collision energy of 35V and an isolation width of 1.3 m/z and adjusted to optimize signal during individual experiments. For the semi-quantitative analysis of PCs and SMs eluted from cleavable CD1, the lipid eluents were normalized based on input protein and 10 µl were injected into a reverse-phase HPLC-MS system (Agilent Poroshell EC-C18 column, 1.9-micron, 3 x 50 mm with an Agilent 6520 QTOF mass spectrometry).(van 't Klooster et al., 2020)")}
Sections "PROJECT" contain missmatched items: {('INSTITUTE', "Brigham and Women's Hospital"), ('INSTITUTE', "Brigham and Women''s Hospital")}
Sections "STUDY" contain missmatched items: {('INSTITUTE', "Brigham and Women's Hospital"), ('INSTITUTE', "Brigham and Women''s Hospital")}
Unable to find '_DATA' block in given files.