Table 2.
Data filters available within ProteoWizard.
| index | <index_value_set> | Selects spectra by index - an index value 0-based numerical order in which the spectrum appears in the input. |
| *msLevel | <mslevels> | Selects only spectra with the indicated MS levels. |
| *chargeState | <charge_states> | Keeps spectra that match the listed charge state. Use 0 to include spectra with no charge state at all. |
| precursorRecalculation | Recalculates the precursor m/z and charge for MS2 spectra based on the MS1 data. Only works on orbitrap and FT data. | |
| precursorRefine | Recalculates the precursor m/z and charge for MS2 spectra based on the MS1 data. Works on Orbitrap, FT, and TOF data. | |
| *peakPicking | <prefer_vendor>, <ms_levels> | Performs centroiding on spectra with the selected MS levels. If used with other filters this must be set first. |
| *scanNumber | <scan_numbers> | Selects spectra by scan number. |
| scanEvent | <scan_event_set> | Selects spectra by scan event. |
| *scanTime | <scan_time_range> | Selects spectra within a given time range. |
| sortByScanTime | Reorders spectra, sorting them by ascending scan start time. | |
| stripIT | Rejects ion trap data spectra with MS level 1. | |
| metadataFixer | Add or replace a spectra’s TIC/BPI metadata, usually after peak picking where the change from profile to centroided data may make the TIC and BPI values inconsistent with the revised scan data. | |
| titleMaker | <format_string> | Adds or replaces spectrum titles according to format string given. |
| *threshold | <type>, <threshold>, <orientation>, [<mslevels>] | Keeps data whose values meet various threshold criteria. Details for the different criteria can be found in the GUI tooltips. |
| *mzWindow | <mzrange> | Keeps mz/intensity pairs whose m/z values fall within the specified range. |
| mzPrecursors | <precursor_mz_list> | Retains spectra with specific precursor m/z values. |
| defaultArrayLength | <peak_count_range> | Keeps only spectra with peak counts within a given range. |
| *zeroSamples | <mode>, [<MS_levels>] | Deals with zero values in spectra - either removing them, or adding them where they are missing. |
| mzPresent | <tolerance>, <type>, <threshold>, <orientation>, <mz_list>, [<include_or_exclude>] | Keeps data whose values meet various threshold criteria. Contains a wider array of options than the “threshold” filter. |
| MS2Denoise | [<peaks_in_window>, [<window_width_Da>, [multicharge_fragment_relaxation]]] | Noise peak removal for spectra with precursor ions. |
| MS2Deisotope | [<hi_res>, [<mz_tolerance>]] | Deisotopes MS level 2 spectra using Markey method. |
| *ETDFilter | [<removePrecursor>, [<removeChargeReduced>, [<removeNeutralLoss>, [<blanketRemoval>, [<matchingTolerance> ]]]]] | Filters ETD MSn spectrum data points, removing unreacted precursors, charge-reduced precursors, and neutral losses. |
| chargeStatePredictor | [<overrideExistingCharge>, [<maxMultipleCharge>, [<minMultipleCharge>, [<singleChargeFractionTIC>, [<algorithmMakeMS2>]]]]] | Predicts MSn spectrum precursors to be singly or multiply charged depending on the ratio of intensity above and below the precursor m/z. |
| *activation | <precursor_activation_type> | Keeps only spectra whose precursors have the specified activation type. |
| analyzer | <analyzer> | Keeps only spectra with the indicated mass analyzer type. |
| polarity | <polarity> | Keeps only spectra with scan of the selected polarity. |