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Articles tagged: Thermo
Spectrum-centric searching of narrow window DIA data with Mascot Server
Data-independent acquisition (DIA) can be broadly separated into narrow window and wide window strategies depending on the size of the isolation window. There are also two data analysis strategies – peptide-centric and spectrum-centric. Wide window DIA typically requires a peptide-centric approach, but narrow window DIA data can be analysed either way. Mascot Server is spectrum-centric, and it’s possible to run [...]
Peak picking intact crosslink spectra with Mascot Distiller
There are several important factors to take into account when carrying out peakpicking for an intact crosslinked dataset. You’ll typically be dealing with higher charge state precursors to handle the larger masses of the linked peptides, and the MS/MS spectra are inherently complex, chimeric spectra with fragments from the alpha and beta peptides. To look at the effects of adjusting [...]
Default or prof_prof? Peak picking Thermo .RAW data with Mascot Distiller
We supply a number of processing options files for each of the main vendor raw file types with Mascot Distiller. These .opt files are designed as a reasonable starting point for peak picking your own data – but to get the very best you’ll need to tweak the parameters on a typical raw file from your instruments and then use [...]