SmartPeak Parameters

This page describes SmartPeak parameters, options and names.

Sample Types

Type	Description
Unknown	todo
Standard	todo
QC	todo
Blank	todo
Double Blank	todo
Solvent	todo
Unrecognized	todo

Metadata

Type	Description
asymmetry_factor	todo
baseline_delta_2_height	todo
calculated_concentration	todo
logSN	todo
peak_apex_int	todo
peak_area	todo
points_across_baseline	todo
points_across_half_height	todo
QC_transition_pass	todo
QC_transition_message	todo
QC_transition_score	todo
QC_transition_group_pass	todo
QC_transition_group_message	todo
QC_transition_group_score	todo
tailing_factor	todo
total_width	todo
width_at_50	todo
RT	todo
leftWidth	todo
rightWidth	todo
scan_polarity	todo
description	todo
modifications	todo
chemical_formula	todo
mz	todo
charge	todo
mz_error_ppm	todo
mz_error_Da	todo
average_accuracy	todo
absolute_difference	todo

Workflow Commands

Raw Data Methods

Type	Description
LOAD_RAW_DATA	Read in raw data mzML file from disk.
LOAD_FEATURES	Read in the features from disk.
PICK_MRM_FEATURES	Run the peak picking algorithm for SRMs/MRMs.
FILTER_FEATURES	Filter transitions and transitions groups based on a user defined criteria.
SELECT_FEATURES	Run the peak selection/alignment algorithm.
VALIDATE_FEATURES	Compare selected features to a reference data set.
QUANTIFY_FEATURES	Apply a calibration model defined in quantitationMethods to each transition.
CHECK_FEATURES	Flag and score transitions and transition groups based on a user defined criteria.
STORE_FEATURES	Write the features to disk.
MAP_CHROMATOGRAMS	Map chromatograms to the loaded set of transitions.
ZERO_CHROMATOGRAM_BASELINE	Normalize the lowest chromatogram intensity to zero.
EXTRACT_CHROMATOGRAM_WINDOWS	Extract out specified chromatogram windows using the componentFeatureFilters.
FIT_FEATURES_EMG	Reconstruct a peak from available data points.
FILTER_FEATURES_RSDS	Filter transitions and transitions groups based on a user defined criteria.
CHECK_FEATURES_RSDS	Flag and score transitions and transition groups based on a user defined criteria.
FILTER_FEATURES_BACKGROUND_INTERFERENCES	Filter transitions and transitions groups based on a user defined criteria.
CHECK_FEATURES_BACKGROUND_INTERFERENCES	Flag and score transitions and transition groups based on a user defined criteria.
EXTRACT_SPECTRA_WINDOWS	Extract out specified spectra windows based on the user parameters.
MERGE_SPECTRA	Merge all spectra along the time axis.
PICK_2D_FEATURES	Run the peak picking algorithm for MS1 spectra.
PICK_3D_FEATURES	Pick 3D Features.
SEARCH_ACCURATE_MASS	Run the accurate mass search algorithm.
MERGE_FEATURES	Create merged features from accurate mass search results.
LOAD_ANNOTATIONS	Read in the annotations from disk.
STORE_ANNOTATIONS	Write the annotations to disk.
CLEAR_DATA	Clear raw and processed data.
STORE_RAW_DATA	Store the processed raw data mzML file to disk.
CALCULATE_MDVS	Calculate MDVs.
ISOTOPIC_CORRECTIONS	Perform Isotopic Corrections.
CALCULATE_MDV_ISOTOPIC_PURITIES	Calculate MDV Isotopic Purities.
CALCULATE_MDV_ACCURACIES	Compare MDVs to Theoretical.

Sequence Segment Methods

Type	Description
CALCULATE_CALIBRATION	Determine the optimal relationship between known sample concentration and measured intensity.
STORE_QUANTITATION_METHODS	Write each transitions calibration model to disk for later use.
LOAD_QUANTITATION_METHODS	Load each transitions calibration model defined in quantitationMethods from disk.
ESTIMATE_FEATURE_FILTER_VALUES	Estimate default FeatureQC parameter values for the feature filters from Standard and QC samples.
ESTIMATE_FEATURE_QC_VALUES	Estimate default FeatureQC parameter values for the feature QCs from Standard and QC samples.
TRANSFER_LOQ_TO_FEATURE_FILTERS	Transfer the upper (u)/lower (l) limits of quantitation (LOQ) values from the quantitation methods to the calculated concentration bounds of the feature filters.
TRANSFER_LOQ_TO_FEATURE_QCS	Transfer the upper (u)/lower (l) limits of quantitation (LOQ) values from the quantitation methods to the calculated concentration bounds of the feature filters.
ESTIMATE_FEATURE_RSDS	Estimate the %RSD for component and component group feature filter attributes from pooled QC samples.
ESTIMATE_FEATURE_BACKGROUND_INTERFERENCES	Estimate the %BackgroundInterferences for component and component group feature filter ion intensity attributes from Blank samples.
STORE_FEATURE_FILTERS	Store the component and component group filters to disk.
LOAD_FEATURE_FILTERS	Load the component and component group filters from file.
STORE_FEATURE_QCS	Store the component and component group QCs to disk.
LOAD_FEATURE_QCS	Load the component and component group QCs from file.
STORE_FEATURE_RSD_FILTERS	Store the component and component group percent RSD filters to disk.
LOAD_FEATURE_RSD_FILTERS	Load the component and component group percent RSD filters from file.
STORE_FEATURE_RSD_QCS	Store the component and component group percent RSD QCs to disk.
LOAD_FEATURE_RSD_QCS	Load the component and component group percent RSD QCs from file.
STORE_FEATURE_BACKGROUND_FILTERS	Store the component and component group percent Background Interference filters to disk.
LOAD_FEATURE_BACKGROUND_FILTERS	Load the component and component group percent Background Interference filters from file.
STORE_FEATURE_BACKGROUND_QCS	Store the component and component group percent Background Interference QCs to disk.
LOAD_FEATURE_BACKGROUND_QCS	Load the component and component group percent Background Interference QCs from file.
STORE_FEATURE_RSD_ESTIMATIONS	Store the component and component group percent RSD estimations to disk.
LOAD_FEATURE_RSD_ESTIMATIONS	Load the component and component group percent RSD estimations from file.
STORE_FEATURE_BACKGROUND_ESTIMATIONS	Store the component and component group percent Background Interference estimations to disk.
LOAD_FEATURE_BACKGROUND_ESTIMATIONS	Load the component and component group percent Background Interference estimations from file.

Sample Group Methods

Type	Description
MERGE_INJECTIONS	Merge multiple injections of the same sample.
LOAD_FEATURES_SAMPLE_GROUP	Load the features for the sample group.
STORE_FEATURES_SAMPLE_GROUP	Store the features for the sample group.

Integrity Checks

Type	Description
SAMPLE	todo
COMP	todo
COMP_GROUP	todo
IS	todo