GPF Creator Quick Reference

GPF Creator is small application that automates the creation of multiple instrument method DIA files to span a precursor range for a gas-phase-fractionation experiment.

• First Precursor
  • The lower bounds precursor m/z
• Last Precursor
  • The upper bounds precursor m/z
• Isolation Width
  • The quadrupole mass filter isolation width. The precursor range is split up into a series of acquisitions having this stride.
• Scan Rate (kDa/s)
  • The ion trap mass analysis rate. This value determines how fast the acquisitions are acquired, and affects the number of experiments needed to span the precursor range.
• LC Peak Width (s)
  • The expected LC peak width at the base. The cycle time is this value divided by the desired points per peak.
• Points per Peak
  • The minimum acquired points per LC Peak width. The cycle time is the LC peak width divided by this value.
• Scan Range Mode
  • Define m/z Range
    • Define an explicit first and last mass for the acquired spectra. The acquisition rate is inversely proportional to the size of the m/z range.

• Define First Mass
  • Define a constant first mass for all acquisitions. The last mass is determined based on the charge state, such that last_mass = precursor_mz * charge + 10

• Auto
  • The first and last mass are determined automatically. The last mass is determined as in the Define First Mass mode. The first mass is determined as the lowest mass that still retains most of the ions at the last mass, based on experimental evaluations.

• Acquisition Time(s)
  • The total estimated amount of time to acquire data for all the acquisitions from the First Precursor to the Last Precursor, with the given settings. The # of Experiments is this value divided by the Cycle Time, rounded up to the next integer.
• Cycle Time (s)
  • The desired cycle time, based on the LC Peak Width / Points per Peak
• Number of Experiments
  • The total number of experiments required to span the Precursor range with the current settings. This is the number of instrument methods that will be created when Create Method Files is clicked.
• Method Template File
  • Double click this text box to open a file chooser for instrument .meth files. The file should have at least one DIA experiment, not counting Adaptive RT experiments (ART). The first non-ART experiment will be modified in the newly created files. The method should have all the LC details desired, and have the appropriate Method Duration and Experiment Durations.

• Create Method Files
  • Click this button to create the instrument methods. Each method will have the name of the template method, with the precursor mass range appended to the end. For example for the gpf_dia.meth template method, files with names like gpf_dia_572to658.meth are created.