Additional Parameters#
Introduction#
There are optional parameters in addition to those detailed in Running a PyParse Analysis which are more rarely re-configured.
Generic Parameters#
- -verbose (-v): “True” or “False”
Specify whether logging should be run in debug mode or not
- -generate_csv (-g): “True” or “False”
Choose whether to generate and save a csv of the outputTable
- -generate_zip (-z): “True” or “False”
Choose whether to generate and save a zip file containing all visualisations and outputs
- -name (-n): String value
Specify a name for the analysis, which appears at the top of the HTML report
Parameters Used for the Analysis#
- -validate (-V): “True” or “False”
Specify whether or not to run the hit validation algorithm.
- -mass_abs_tol (-mat): Float value
How close an observed m/z should be to a calculate mass to be considered a match
- -time_abs_tol (-tat): Float value
How close two retention times should be to be considered part of the same cluster/relate to the same compound
- -uv_abs_tol (-uat): Integer value
How close should the wavelengths of the maxima in a UV absorption profile be for two eluting peaks to be considered a match
- -min_peak_area (-mpa): Float value
Minimum percentage UV peak area required for inclusion in analysis
- -min_massconf_threshold (-mmt): Integer value
The lowest mass confidence (percentage height of m/z peak divided by the sum of percentage heights of all observed m/z peaks) at which a hit will still be recorded.
- -min_uv_threshold (-mut): Integer value
Minimum height of a peak in the UV absoption profile (AU vs wavelength) required to be saved for use in the hit validation algorithm.
- -uv_match_threshold (-umt): Float value
Parameter to determine how many UV maxima a hit needs to match those found for the bulk values before it is considered a tentative hit and flagged to the user for further analysis.
- -uv_cluster_threshold (-uct): Float value
Parameter to determine how many times a UV maximal wavelength should be observed for a compound (across all hits in a cluster) compared to the number of times the most commonly observed wavelength is seen, as a fraction, to be considered a “required value” for that compound.
- -massconf_theshold (-mt): Float value
The value for which, when it’s multiplied by the mean mass confidence for a cluster, the mass confidence for a hit in that cluster is deemed too small and is flagged to the user for further analysis.
- -cluster_size_threshold (-cst): Float value
The value for which, when it’s multiplied by the number of hits in the largest cluster, the number of hits in a cluster is deemed too small and is discarded from further analysis.
- -min_no_of_wells (-now): Integer value
Minimum number of hit-containing wells required for a compound to allow the full validation process to run.
- -mass_or_area (-moa): “mass_conf” or “area”
Parameter to determine how which hit is chosen when more than one hit is found in a well for a compound
- -calc_higherions (-chi): “True” or “False”
Use [M+2H]2+ and [M+3H]3+ ions when looking for hits for a compound. Specify when a set of compounds are likely to ionise multiple times on the mass spectrometer.
- -calc_boc (-cboc): “True” or “False”
Look for Boc degradation ions when looking for hits for a compound
- -filter_by_rt (-f): String value
Provide retention time ranges to ignore, written as ‘mintime-maxtime’ where the two times are separated by a hyphen. Multiple ranges may be specified by a space.
- -detector (-d): String value, “UV” or “ELSD”
Specify “ELSD” where required to use only ELSD detector data for the analysis. Default is “UV”, where only UV detector data are used. Waters data option only.
- -find_freq_imp (-ffi): “True” or “False”
Choose whether to search for and report frequently observed impurities. Automatic Impurity Detection and Reporting
Parameters Used for the Visualisations#
- -points_per_trace (-ppt): Integer value
The maximum number of data points of a UV chromatogram to save. This value should be reduced if the program is found to run exceptionally slowly.