Maxis 4g qq tof mass spectrometer

CE–ESI
MS/MS was performed as reported previously^{27 (link)} using both an Impact HD or a maXis 4G Qq-ToF mass spectrometer (Bruker
Daltonics) operated in positive and negative ion modes. Biofilm extracts
were prepared by collecting ∼1 mg of dried biofilm from the
silicon substrate with a clean razor blade, depositing the film into
a microcentrifuge vial, adding 20 μL of extraction solution
(50/50 (v/v) MeOH:H₂O + 0.5% AcOH), shaking vigorously
for 2 min, then centrifuging for 5 min at 2000g.
For each run, 6 nL of supernatant was loaded into a capillary (65–70
cm long) and a separation potential of 15 kV applied. For negative
ion mode analysis, CE was performed using a background electrolyte
composed of 20 mM ammonium bicarbonate, and a sheath liquid of 60%
(v/v) isopropyl alcohol and 200 μM ammonium bicarbonate, delivered
at 600 nL per minute. Instrument calibration was performed using sodium
acetate clusters in negative ion mode. Molecular features were assigned
with high confidence through matching of the tandem mass spectral
data from the endogenous substances with those found at publicly available
mass spectral databases (METLIN^{28 (link)}).

CE–MS
was performed as reported
previously^{31 (link)} using either a micrOTOF or
a maXis 4G Qq-ToF mass spectrometer (Bruker Daltonics, Billerica,
MA) operated in positive ion mode. The current procedure differed
from our prior work in that we used a capillary length of 65–70
cm, a separation potential of 14–16 kV, and a sample injection
volume of ∼28 nL. Over 100 distinct molecular features were
detected from the cytoplasm samples, among which 70 metabolite identities
were assigned with high confidence through spiking with standards,
migration order agreement, and matching of tandem mass spectral data
from the endogenous substances with those of chemical standards when
available and with fragmentation profiles found at publicly available
mass spectral databases (Metlin^{32 (link)} and HMDB^{33 (link)}). A signal-to-noise ratio of 3 was used as the
threshold of detection for an analyte while using an isolation width
of ±10 mDa; the migration time also had to match the standard
within the typical variation in migration times for other compounds
within each CE run.