Submit mass-based fraction collection (MBFC) runs
Click here to see this page in full context

Submit mass-based fraction collection (MBFC) runs

You can submit MBFC runs via the sequence.

Dedicated columns are proposed to you (override method parameters mechanism), that can be chosen in the column chooser / Method Override Columns.

Two MBFC Workflows are supported:

  • Submit run (= sequence line) using the MBFC parameters defined in the acquisition method (Mass detector & Fraction collector sections). Define the acquisition method and information such as vial or fraction location in the sequence. You cannot add dedicated MBFC parameter values at this point. If you want to collect fractions based on different target masses for example, you have to define separate acquisition methods in sequence lines.

  • Submit MBFC runs using an acquisition method but override the method target masses and/or fraction collector thresholds values by values defined in the sequence. Values defined in the sequence are used to perform the analysis, acquisition method parameters are not modified. This workflow allows you to use the same acquisition method in the lines of the sequences and define Target masses and/or Fraction collector threshold to be used for each line in the dedicated columns.

The override method parameters are validated against the acquisition method defined in the sequence line.

Target masses override parameter

For Mass detector, the sequence columns SQ: T1 Fraction target mass 1 to SQ: T3 Fraction target mass 3 override the monoisotopic masses from the instrument setup in the acquisition method. All other parameters defined in the acquisition method in the Mass-based fraction collection parameters table (adducts, ionization mode, fragmentor, gain, etc.) are applied.

The values defined in the sequence columns SQ: Ti Fraction target mass i (Ti= T1, T2 or T3) override the target masses defined in the corresponding Ti section.

Example: Mass-based fraction collection parameters
Figure Example: Mass-based fraction collection parameters
Example: adducts for an MS target compound
Figure Example: adducts for an MS target compound

For example, if you define SQ: T1 Fraction target mass 1 =622.5 in sequence, a fraction will be collected when the mass 622.5 +1=623.5 (adduct =H+, mass=1) or 622.5+23=645.5 (adduct =Na+, mass=23) is detected by the mass detector.

You can define several target masses per cell using the following syntax:

  • mass (e.g. 78.11)

  • couple compound name| mass (e.g. Benzen|78.11)

  • formula (e.g. C6H6)

  • couple compound name| formula (e.g. Benzen|C6H6)

  • Several target masses separated by a semicolon

Example

Threshold override parameter

For a fraction collector, you can override the thresholds defined for signals 1 to 4 in the method by values defined in the sequence columns Fraction Collector: Threshold MS 1 to Fraction Collector: Threshold MS 4 . A number is expected.

Both overridden target masses and overridden threshold values will be displayed in Data Analysis in the Acquisition Setpoints  > Overridden Method parameters window.

×