Easitag and TopNΒΆ


EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification Sebastian Virreira Winter, Florian Meier, Christoph Wichmann, Juergen Cox, Matthias Mann & Felix Meissner doi: 10.1101/225649

The EasiTag strategy is based on the standard topN strategy but has some modifications and extensions. 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
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