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. Author manuscript; available in PMC: 2014 Jun 15.
Published in final edited form as: Methods. 2013 Apr 21;61(3):251–259. doi: 10.1016/j.ymeth.2013.04.010

Table 1.

Experimental settings of LTQ-Orbitrap XL used in phosphoproteomic analysis.

Parameters of LTQ- Orbitrap XL Experimental settings* Allowed range Notes
Resolution 60,000 7500– 100,000

  • At higher resolution, slower scan speeds
AGC target value of Orbitrap 800,000 (Orbitrap)
30,000 (LTQ)

  • Prevents over-filling of ion trap
Minimum signal threshold(counts) 15,000 0–10E(9)

  • Minimum ion count cutoff for precursor ion selection for MSMS

  • Optimized to the average ion count noise level
Maximal ion accumulation time 500 ms (Orbitrap)
250 ms (LTQ)

  • Maximum allowed time for filling ion trap before reaching the AGCs
Duration of dynamic exclusion 30–60 sec

  • Period of time that ions remain excluded from precursor ion selection for MSMS

  • Optimized at the average LC peak width at half height
Normalized collision energy (CID) 30% 0–100%

  • Applied energy for ion fragmentation

  • Set at the maximum fragmentation efficiency
Activation time (CID) 30 ms

  • Applied activation time for ion fragmentation

  • Set at the maximum fragmentation efficiency
*

Values typically used for phosphoproteome analysis.