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The LTQ Orbitrap Velos was operated in data-dependent mode, using a full scan in the Orbitrap (m/z range 380 1650, nominal resolution of 60,000, target value 1E6) followed by MS/MS scans of the 12 most abundant ions in the linear ion trap.
The LTQ FT was operated in data-dependent mode using a full scan in the ICR cell (m/z range 400 1800, nominal resolution of 100,000 at m/z 400, ICR target value 500,000) followed by MS/MS scans of the five most abundant ions in the linear ion trap.
Detection was accomplished using a full scan multi channel ESA Coulometric detector in the "oxidative-screen" mode with the upstream electrode (E1) set at +600 mV and the downstream (analytical) electrode (E2) set at +950 mV, while the potential of the guard cell was maintained at +1050 mV.
Peptides were eluted with a linear gradient of buffer B; 4% B was first applied, followed by a linear gradient to 50% B in 105 min, and then to 100% B in 9 min, holding at 100% B for an additional 6 min. MS/MS spectra were acquired using a full scan followed by five MS/MS scans on the five most intense precursor ions in data-dependent mode.
Peptides were eluted initially with 100% A for 1 min, then 90% A for 5 min, then a linear gradient to 55% A by 60 min, then to 0% A at 70 min and held to 80 min, then to 100% A at 80.01 min and held until 90 min. MS/MS spectra were acquired by using a full scan followed by five MS/MS scans in a data-dependent mode.
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Apart from the scan style, the designer also needs to consider the scan methodology involved, and make a decision on whether to use a full scan method or a partial scan method.
MS data were collected in 'triple-play' mode, which uses a full scan at 400 2000 m/ z for selection of the three most predominant eluting peptides, followed by a high resolution zoom scan, and MS/MS (tandem MS) of the respective isolated peak of interest.
Spots that were deemed unique were further scanned using a full XANES scan.
Orbitrap spectra (AGC 1×106) were collected using a full range scan of 400 2000 m/z at a resolution of 100k followed by the data dependent ion trap MS/MS spectra (AGC 1×104) of the three most abundant ions using a collisional energy of 35%.
As noted in the Introduction, Leamy et al. (2008) detected a large amount of epistasis using a full genome scan of SNP markers in an F2 population of mice derived from a cross of two inbred strains, and some of the epistatic interactions involved markers on the X chromosome.
A two-QTL model was also fitted to the data using a full two-dimensional scan of each chromosome in QTL Express [ 30].
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