Full MS / dd-MS² (TopN)
General
Runtime                                                              0 to 46 min
Polarity                                                            Positive 
In-source CID                                                            0.0 eV
Default charge state                                                       1 
Inclusion                                                                  ― 
Exclusion                                                                  ― 
Tags                                                                       ― 
Full MS
Microscans                                                                 1 
Resolution                                                            70,000 
AGC target                                                               1e6 
Maximum IT                                                               250 ms
Number of scan ranges                                                      1 
Scan range                                                        70 to 1050 m/z
Spectrum data type                                                   Profile 
dd-MS² / dd-SIM
Microscans                                                                 1 
Resolution                                                            35,000 
AGC target                                                               2e5 
Maximum IT                                                               120 ms
Loop count                                                                 5 
MSX count                                                                  1 
TopN                                                                       5 
Isolation window                                                         4.0 m/z
Isolation offset                                                         0.0 m/z
Scan range                                                       200 to 2000 m/z
Fixed first mass                                                           ― 
NCE / stepped NCE                                                         65 
Spectrum data type                                                   Profile 
dd Settings
Underfill ratio                                                         20.0 %
Intensity threshold                                                    3.3e5 
Apex trigger                                                               ― 
Charge exclusion                                                           ― 
Peptide match                                                            Off 
Exclude isotopes                                                          on 
Dynamic exclusion                                                       10.0 s
If idle ..                                                do not pick others 

Negative mode is the same but with Negative polarity. TopN is the number of things it
fragments, NCE is the collision energy, it uses such a large isolation window as it is a
quadrupole that picks the ions. There is no in-source CID. 10s dynamic exclusion so it
doesn’t constantly fragment the same peak. The AGC is the automatic gain control, the
idea is that once it has collected that number of ions it’ll inject them into the
orbitrap, the maximum IT is a hard limit on cycle time, meaning it will inject after that
no matter how many ions it has, so it doesn’t sit idle if it can’t reach the AGC.
Resolution is lower during MS2 to improve sensitivity.