Thermo finnigan ltq

The first experiment was completed using the first set of samples (N = 48) (referred to as “batch 1”).
Metabolite extraction and detection as previously described (10 (link)). Briefly, liver sample preparation was conducted using a proprietary series of organic and aqueous extractions to remove the protein fraction and optimize recovery of small molecules through the automated MicroLab STAR® system (Hamilton Company, UT, USA), centrifuged, and the resulting supernatants were analyzed by analyzed by ultra-performance liquid chromatography mass spectrometry (UPLC-MS/MS) in a positive and negative ion mode (UPLC: Waters, Milford, MA; mass spectrometer: Thermo-Finnigan LTQ, Thermo Fisher Scientific, Waltham, MA, scan range, 80–1,000 m/z) and by GC-MS (Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer, scan range 50–750 m/z). The final experiment 1 metabolomic dataset comprised a total of 751 biochemicals, 478 compounds of known identity (named biochemicals) and 273 compounds of unknown structural identity. As initial statistical analysis revealed an age-dependent effect that could not be distinguished from a tissue source-related effect, a replication set of group 1 samples was obtained through collaboration with the Erasmus Medical Center/Sophia Children's Hospital.

Metabolite extraction and detection were performed at Metabolon Inc. (Durham, NC, USA) as previously described [54 (link)]. FF and OVS samples (100 μL) were extracted through the automated MicroLab STAR^® system (Hamilton Company, Bonaduz, Switzerland), and centrifuged. The resulting supernatants were analyzed by UPLC-MS/MS in a positive and negative ion mode (UPLC: Waters, Milford, MA, USA; mass spectrometer: Thermo-Finnigan LTQ, Thermo Fisher Scientific, Waltham, MA, USA, scan range, 80–1000 m/z) and by GC-MS (Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer, scan range 50–750 m/z).

lncRNA CBR3-AS1 interacted proteins performed LC–MS/MS analyzed by Thermo Finnigan LTQ linear ion trap mass spectrometer (Thermo Fisher Corporation, San Jose, CA) in line with a Thermo Finnigan Surveyor MS Pump Plus HPLC system. The mass spectrometry analysis was carried out in a data-dependent mode with an automatic switch between a full MS and an MS/MS scan in the obitrap. Peptide sequences were searched using trypsin specificity and allowing a maximum of two missed cleavages. Sequest was searched with a peptide tolerance of 3.0 Da and a fragment ion tolerance of 1.0 Da. The results of peptide sequences information of CBR3-AS1 interact proteins were offered in Additional file 3: Table S2.