With thermo fusion lumos, which codes should I use in instrument option?

[TnakaNY]

Hi,

I am going to analyze a data derived from Thermo Fusion Lumos by MSGF+.

In instrument code, MSGF+ has below; 0: Low-res LCQ/LTQ (Default), 1: Orbitrap/FTICR, 2: TOF, 3: Q-Exactive

Which code should I use for Fusion Lumos data?

Best, TnakaNY

[alchemistmatt]

I agree, the difference between mode 1 (Orbitrap) and mode 3 (Q-Exactive) is a bit nebulous. Likely the scoring model was trained with a different set of training data. ~Most likely the Q-Exactive scoring model was trained with high res MS1 / high res MS2 datasets. If your Fusion Lumos data is high/high, mode 3 is likely better. If it is high res MS1 / low res MS2 (using the ion trap), then mode 1 is better.~

Of course, it wouldn't hurt to try both modes with your data and see which gives more high confidence identifications.

[alchemistmatt]

Correction. I just looked at my automation code and it uses the following logic:

• If the instrument is a QExactive, use mode 3
• If the instrument has HCD spectra (which should be high res MS2), use Mode 1
• If the instrument has high res MS2 spectra, use Mode 1
• If the instrument has low res MS2 spectra, use Mode 0

You can tell if the MS2 spectra are high res by looking for FTMS in the scan filter, for example FTMS + p NSI. Low res spectra have ITMS in the scan filter. Thus, for your Fusion Lumos data use mode 1.

[TnakaNY]

Hi, Thank you for your quick reply! I will change my instrumental code to 1 from 3.

Very best, TnakaNY