Thermo qe hf mass spectrometer

The samples were separated by ultra-high-performance liquid chromatography (UHPLC) and analyzed by mass spectrometry using a Thermo QE HF mass spectrometer (Thermo). Electrospray ionization (ESI)-positive and ESI-negative ion modes were used for detection. In addition, the MSdial program was used for peak data extraction, and the SIMCA program was used for principal component analysis (PCA) and orthogonal partial least-squares discrimination analysis (OPLS-DA). Subsequently, metabolite structure identification was performed using exact mass number matching, secondary spectrum matching, and public databases. Differential metabolites were categorized using the Human Metabolome Database (HMDB, http://www.hmdb.ca/).

Except the large protein samples that required the extended mass range offered by Bruker RapifleX MALDI-TOF/TOF instrument (Bruker Daltonik, Bremen, Germany; with standard configurations and operations except the modification with NBA), the remaining experiments were carried out on a Thermo QE-HF mass spectrometer (Thermo Fisher Scientific, Bremen, Germany). The SubAP-MALDI source was coupled with QE-HF mass spectrometer for most data acquisition. The Target-ng software (MassTech, Columbia, MD) was used to control the ion source and ion funnel. For spot analysis, an ABI Opti-TOF 192 target plate (Applied Biosystems, Foster City, CA) was employed to allow spotting the peptide standards and matrix solutions. While spiral plate motion was used in spot analysis, constant speed raster motion was used for MSI. The MS was operated under positive polarity mode, with mass range of m/z 500–6000 and mass resolution of 60,000 unless otherwise specified. To ensure consistent scan time at each pixel, the maximum injection time was set to 300 ms and automatic gain control target was tuned to 3e6.