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A high precision electric field simulation method is employed to investigate micron-size geometry deviation effects on the electric field distributions as well as on mass resolutions in linear ion traps.
Electrode misalignments in linear ion traps have a strong effect on performance but are hard to fully test in experiments due to limitations of mechanical accuracy and the large number of degrees of freedom in traps with multiple electrodes.
MALDI-TOF instrument was operated in linear ion mode.
All measurements were performed in the m/z range of 1,000 10,000 in linear ion mode.
Samples were analyzed in linear ion mode in the m/z range of 1,000 10,000 to cover the expected masses of all peptides (2.3 to 9.1 kDa).
Low resolution MS/MS spectra were acquired in Linear Ion Trap in a data-dependent manner – the top 10 precursors (in terms of abundance) were fragmented using CID fragmentation at a normalized collision energy of 35.
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MS/MS was performed in linear ion-trap on the six most abundant multiple charged ions for each scan (one microscan, maximum 200 ms injection and an AGC of 30000) using CID (collision-induced dissociation) fragmentation at 30% normalized collision energy.
Thus, the analysis of large peptides by MRM in linear ion-trap mass spectrometers can be performed with improved detection limits, due to the formation of fewer but more intense product ions in the ion trap vs. the triple quadrupole [ 25, 26].
The five most abundant ions from every full-scan over the range 340 1800 m/z at 60000 resolution in the Orbitrap analyzer were fragmented by MS/MS in parallel in the linear ion trap LTQ (MS/MS).
MS/MS-spectra were acquired in the linear ion trap in centroid mode.
The four most intense ions were selected in data-dependent mode and fragmented in the linear ion trap, with settings as in Ali, et al. [ 58].
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