This filter selects spectra by scan event. is an int_set of scan numbers to be kept. Depending on the input data type, scan number and spectrum index are not always the same thing - scan numbers are not always contiguous, and are usually 1-based. This filter selects spectra by scan number. is a low-quality (non-vendor) local maxima algorithm The other option for PickerType is "cwt", which uses ProteoWizard's wavelet-based algorithm for performing peak-picking with a wavelet-space signal-to-noise ratio of. IMPORTANT NOTE: since this filter operates on the raw data through the vendor DLLs, IT MUST BE THE FIRST FILTER IN ANY LIST OF FILTERS when "vendor" is used.
#FILTER FORGE 5 0 CODE#
The value for must be "cwt" or "vendor": when = "vendor", vendor (Windows DLL) code is used if available. This filter performs centroiding on spectra with the selected, expressed as an int_set. It does not use any 3rd party (vendor DLL) code. It only works on orbitrap, FT, and TOF data. It looks at the prior MS1 scan to better infer the parent mass. This filter recalculates the precursor m/z and charge for MS2 spectra. Distinct m/z value for negative ions is optional and defaults to the given mz value. Recommended Score and thresholds: MS-GF:SpecEValue,-1e-10 (35) xcorr,3- (>3)įor Waters data, adjusts m/z values according to the specified lockmass m/z and tolerance. It is designed to work on mzML files created by msconvert from a single dataset (single run), and with an identification file created using that mzML file.
It uses an ident file with a threshold field and value to calculate the error and will then choose a shifting mechanism to correct masses throughout the file. This filter recalculates the m/z and charges, adjusting precursors for MS2 spectra and spectra masses for MS1 spectra. Since the time the code was written, Thermo has since fixed up its own estimation in response, so it's less critical than it used to be (though can still be useful). However, it only works on orbitrap and FT data,although it does not use any 3rd party (vendor DLL) code. Use 0 to include spectra with no charge state at all. Both known/single and possible/multiple charge states are tested. This filter keeps spectra that match the listed charge state(s), expressed as an int_set. This filter selects only spectra with the indicated, expressed as an int_set. Selects spectra by index - an index value 0-based numerical order in which the spectrum appears in the input. '9' is also an integer set, equivalent to ''. '1-' means 'the set of integers from 1 to the largest allowable number'. An int_set is a set of integers written as a list of intervals of the form or a.įor example '' and '0-3' both mean 'the set of integers from 0 to 3 inclusive'. In particular, the peakPicking filter must be first in line if you wish to use the vendor-supplied centroiding algorithms since these use the vendor DLLs, which only operate on raw untransformed data. Where filtername is the literal name of the filter and filterargs is a list of arguments that you replace with actual values.įor example, the "index" filter as described below would be used like this in the msconvert program:įilters are applied sequentially in the order that you list them, and the sequence order can make a large difference in your output. ProteoWizard Technical Documentation: Filters Filters as used in msaccess, msconvert, and other ProteoWizard toolsĮach filter entry listed below has the form