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Mobile phases consisted of 0.1% formic acid (A) and MeOH (B) with isocratic elution at 50 50 (v/v) at a flow rate of 0.4 mL min-1 for 1 min. Electrospray ionization (ESI) was performed in positive ion mode from m/z 100 to 700 using the linear ion trap (LIT) operating under enhanced MS (EMS) mode.
Where specified, targeted MSn experiments were performed using collision-induced dissociation (CID) mode using the linear ion trap analyzer of the LTQ Orbitrap machine [24], [29].
Full spectra (600 2000 m/z range) were collected on a Thermo Orbitrap Discovery XL in profile mode using the linear ion trap analyzer (ITMS mode).
For final structural elucidation, samples were injected on an LC-ESI-XL-Orbitrap (Thermo, Steingrund, Germany) using the linear ion trap for fragmentation.
In each duty circle of mass analysis, one high-mass resolution (100 000) MS spectrum was acquired using the FT-ICR analyzer, followed by five data-dependent MS/MS scans using the linear ion trap analyzer.
Therefore, we also recorded MS/MS spectra of the TGM2 modified (Fig 2c) and non-modified (Fig 2d) peptides using the linear ion trap (LIT) mode of the Qtrap instrument.
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I'm using the linear method".
Digestion products were eluted using a gradient from 5%B to 99%B in 49 min, followed by 99% B for 5 min. RNase T1 digestion products were analyzed using the Thermo LTQ-XL linear ion trap mass spectrometer.
MS/MS experiments were performed using collision-induced dissociation in the linear ion trap, and the fragment ions were detected in the orbitrap analyzer operated under the target mass resolution of 30,000 (FWHM, defined at m/z 400).
The method used allowed sequential isolation of the most intense ions (up to five, depending on signal intensity) for fragmentation on the linear ion trap using collisionally induced dissociation at a target value of 100,000 charges.
Nineteen different proteins were identified, most of them by using the ESI-linear ion trap instrument in combination with a nano-HPLC.
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