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For every peptide, fragmentation was performed by CID and ETD, and spectra acquired in both the linear ion trap and the FT-Orbitrap.
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Using the MALDI Orbitrap ion isolation and collisional dissociation were achieved in the linear ion trap, and both precursor and product ions were detected in the Orbitrap.
The method allowed sequential isolation of up to the 7 most intense ions for fragmentation on the linear ion trap using collision induced dissociation (CID) at a target value of 10,000 charges.
The improvements have been proposed on the linear ion drift [3], non-linear ion drift [46], Yakopcic [73, 74], TEAM/VTEAM [75 77], and ASU [78] models.
Window functions are introduced in the "Linear Ion Drift Model" section [3].
Precursor ions were isolated and subjected to CID in the linear ion trap.
The six most intense ions were sequentially isolated for fragmentation and detection in the linear ion trap.
The six most intense ions of a full MS acquired in the orbitrap analyzer were fragmented and analyzed in the linear ion trap.
Precursor masses were collected at high resolution; MS/MS spectra were triggered for the ten most abundant ions and acquired in the linear ion trap.
Up to 5 most intense multiply charged ions (2+, 3+ or 4+) per scan were CID fragmented in the linear ion trap.
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].
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