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Update appEasiTag.rst
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christophwi committed Oct 31, 2018
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Expand Up @@ -8,68 +8,60 @@ The EasiTag strategy is based on the standard topN strategy but has some modific
In EasiTag, the precursor selection is more stringent and only select monoisotopic peaks for fragmentation.
Furthermore, the isolation windows are shifted by a global offset and their size chosen to be charge state dependent.

+-----------------------------+----------------------------------------------------------------------------------------------------+
| Method parameter | Description |
+=============================+====================================================================================================+
| **General** | |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| BoxCar Scans | Number of BoxCar scans per acquisition cycle |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| BoxCar Boxes | Number of boxes per BoxCar scan |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| BoxCar overlap | M/z overlap of neighboring boxes (Th) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| ScanDataAsProfile | Profile (true) or centroid (false) spectra |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| Positive mode | Electrospray polarity |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| **Full Scan settings** | |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| MaxIT | Maximum ion injection time (ms) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| Resolution | MS resolving power at m/z 200 |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| AGCtarget | AGC target value (charges) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| MzRange | Scan range (m/z) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| **BoxCar scan settings** | |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| MaxITBoxCar | Maximum total ion injection time (ms) for BoxCar scans. Each box is assigned 1/N th of this value. |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| ResolutionBoxCar | MS resolving power at m/z 200 |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| AgcTargetBoxCar | Total AGC target value for each BoxCar scan (charges). Each box is assigned 1/N th of this value. |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| MzRangeBoxCar | Scan range (m/z) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| **Fragmentation** | |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| NumOfPrecursors | Number of precursor ions per acquisition cycle |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| Normalized collision energy | Normalized collision energy (NCE) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| DynamicExclusion | Dynamic exclusion time of precursors after first spectrum (s) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| Exclusion mass tolerance | Mass tolerance for dynamic exclusion (ppm) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| Exclusion threshold | Intensity threshold for dynamic exclusion |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| Isolation window | Width of the precursor isolation window (Th) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| MinCharge | Minimum charge state of the precursor |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| MaxCharge | Maximum charge state of the precursor |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| Intensity threshold | Precursor intensity threshold (cps) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| MinMass | Minimum mass threshold for precursor ions (Da) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| **Ms2 scan settings** | |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| MaxIT | Maximum ion injection time (ms) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| Resolution | MS resolving power at m/z 200 |
+-----------------------------+----------------------------------------------------------------------------------------------------+
| AgcTarget | AGC target value (charges) |
+-----------------------------+----------------------------------------------------------------------------------------------------+
+-----------------------------------+---------------------------------------------------------------------+
| Method parameter | Description |
+===================================+=====================================================================+
| **General** | |
+-----------------------------------+---------------------------------------------------------------------+
| NumOfPrecursors | Number of precursor ions per acquisition cycle |
+-----------------------------------+---------------------------------------------------------------------+
| DynamicExclusion | Switch for dynamic exclusion |
+-----------------------------------+---------------------------------------------------------------------+
| ExclusionDuration | Dynamic exclusion time of precursors after first spectrum (s) |
+-----------------------------------+---------------------------------------------------------------------+
| ExclusionThreshold | Mass tolerance for dynamic exclusion (ppm) |
+-----------------------------------+---------------------------------------------------------------------+
| LifeTime | Max time a MS2 scan stays in the queue (ms) |
+-----------------------------------+---------------------------------------------------------------------+
| Isolation window | Width of the precursor isolation window (Th) |
+-----------------------------------+---------------------------------------------------------------------+
| MinCharge | Minimum charge state of the precursor |
+-----------------------------------+---------------------------------------------------------------------+
| MaxCharge | Maximum charge state of the precursor |
+-----------------------------------+---------------------------------------------------------------------+
| Intensity threshold | Precursor intensity threshold (cps) |
+-----------------------------------+---------------------------------------------------------------------+
| MinMass | Minimum mass threshold for precursor ions (Da) |
+-----------------------------------+---------------------------------------------------------------------+
| MzOffset | Offset that is added to the peak mz-value (Th) |
+-----------------------------------+---------------------------------------------------------------------+
| UseChargeSpecificIsolationWindows | Switch to enable charge specific isolation windows |
+-----------------------------------+---------------------------------------------------------------------+
| IsolationWindowList | Define isolation windows widths for every allowed charge state |
+-----------------------------------+---------------------------------------------------------------------+
| ScanDataAsProfile | Profile (true) or centroid (false) spectra |
+-----------------------------------+---------------------------------------------------------------------+
| **MS1 Scan settings** | |
+-----------------------------------+---------------------------------------------------------------------+
| PositiveMode | Ion polarity |
+-----------------------------------+---------------------------------------------------------------------+
| MaxIT | Maximum ion injection time (ms) |
+-----------------------------------+---------------------------------------------------------------------+
| Resolution | MS resolving power at m/z 200 |
+-----------------------------------+---------------------------------------------------------------------+
| AGCtarget | AGC target value (charges) |
+-----------------------------------+---------------------------------------------------------------------+
| MzRange | Scan range (m/z) |
+-----------------------------------+---------------------------------------------------------------------+
| **Ms2 scan settings** | |
+-----------------------------------+---------------------------------------------------------------------+
| MaxIT | Maximum ion injection time (ms) |
+-----------------------------------+---------------------------------------------------------------------+
| Resolution | MS resolving power at m/z 200 |
+-----------------------------------+---------------------------------------------------------------------+
| NCE | Normalized collision energies (whitespace separated - only EasiTag) |
+-----------------------------------+---------------------------------------------------------------------+
| AgcTarget | AGC target value (charges) |
+-----------------------------------+---------------------------------------------------------------------+
| LowerMzBound | Lower Mz boundary for Ms2 spectra |
+-----------------------------------+---------------------------------------------------------------------+

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