Commands:
Tools > Tasks > Precursor
Tools > Tasks > Ion Group
Tools > Tasks > Mascot Search
View > Unlink Fragment Spectra


The tasks window lists a series of data processing methods.

Simulation of Precursor Selection
The command Tools > Tasks > Precursor opens the precursor selection simulation pane. This task simulates the selection of ions for fragmentation throughout a chromatographic tandem MS run.
  • The m/z Range is the m/z range from which an ion will be selected.
  • The Intensity Threshold (absolute or relative) is the intensity threshold for selection. No ion with an intensity below the higher of the two values will be selected for fragmentation.
  • The Precursor Exclusion defines which ions will not be selected based on their m/z values.
  • The dynamic exclusion time defines a time for which the m/z values of all formerly selected ion m/z values will not be selected for a second time.
  • The fixed exclusion list defines m/z values that will never be selected.
  • The Charge State options define which potential ion will be excluded or selected based on their charge state as determined in real time on the available data. "Real time" charge state determination might not always be correct.
  • The Process Simulation options list in preselected precursors how many precursors will be fragmented before a new mass spectrum is acquired.
  • The acquisition time is the time the mass spectrometer will require (on the average) to acquire a single fragment spectrum.

Ion Group Comparison
The command Tools > Tasks > Ion Group opens the ion group comparison pane. This task compares two ion groups in the active Arcadiate data collection.
  • The Reference Group is selected by activating an ion group in a data collection and pressing the Active Group button.
  • The Compared Group is selected in the same way.
  • Tolerance in m/z is the m/z window within which two ions are considered to have the same m/z value
  • Tolerance in Time is the width of the time window within which two ions are considered to have the same retention time

Database Search Significance Level
The command Tools > Tasks > Mascot Search activates the database search significance panel. This task determines a score threshold for a given false positive rate.
  • Database searches are selected by activating a Database Search Result view in a data collection and pushing the button Active Search
  • The Tolerated False Positive Rate gives the percentage of statistically tolerated false positives in the results from the real database

All peptide identifications with a score higher than the determined score threshold will be considered to be significant identifications. The score threshold is calculated by comparing the search in the real database with the search in a decoy database. Using a tolerated false positive rate the score threshold is reached when the number of identifications in the decoy database with scores higher than the threshold divided by the number of identifications in the real database with scores higher than the threshold remains just below the tolerated false positive rate.
The determined score threshold can be used with the command View > Unlink Fragment Spectra to dissociate all sequences from their assigned fragment spectra below this score. This type of significance level determination is appropriate for search results with many identifications.