FAQ

This is a list of Frequently Asked Questions about SmartPeak.

What types of experiments does SmartPeak support?

SmartPeak supports various types of analytical chemistry experimental designs. The experimental designs are specified in the sequence file by the ordering and grouping of sample types.

An example of a sequence for a bracketed experimental design common to targeted quantification experiments is provided below.

Bracketed sequence

All Blank, QC, Standard, and Unknown sample types that are a part of the same sequence segment are processed together. This means that e.g., background estimation, QC variance calculations, and quantitation method calculations are calculated based off of the samples that are in the same sequence segment and applied to the samples in the same sequence segment.

The different sample types that can be specified by the user are given below.

Sample types

Type	Description
Unknown	Normal samples of unknown concentration
Standard	Samples of known concentration. These samples are used for the creation of the calibration curve.
QC	Quality Controls. SmartPeak supports two types of quality control samples: 1) analytical controls and 2) process controls. Analytical controls are samples of known concentration are used to check the accuracy of the calibration curve but do not influence its actual construction. Process controls are a mix of biological replicates that are representative of the dataset and that are injected at standard intervals to estimate the variance given in the same matrix during the run.
Blank	These are generally samples containing the internal standard compounds, if used, but no analytes, and which have been through the normal sample preparation procedure.
Double Blank	These are samples with neither internal standards nor analytes.
Solvent	These are double blanks that have not been through the normal sample work-up procedure.
Unrecognized	User specified sample type that is not recognized by SmartPeak.

What are the different types of data processing workflows that SmartPeak supports?

SmartPeak supports data processing workflows for quantitation, phenotyping, and discovery analytical chemistry applications. Specifically, single reaction monitoring (SRM), single ion monitoring (SIM), full scan, data-dependent acquisition with product ion scans based off of SRM or full scan survey scans, and data-dependent acquisition (e.g., SWATH) with or without liquid or gas chromatography are supported. High performance liquid chromatography (HPLC) with refractive index (RI) or ultra violet (UV) detection are also supported. Data processing preset workflow for each of the supported workflows are available in SmartPeak. The preset workflows can be customized by the user and saved for later re-use. The available workflow steps are listed below.

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.

What types of feature metadata does SmartPeak record?

Various feature metadata is calculated and recorded during workflow execution, and made available for viewing and reporting after workflow execution.

Feature metadata

Type	Description
tailing_factor	The tailing factor is a measure of peak tailing. It is defined as the distance from the front slope of the peak to the back slope divided by twice the distance from the center line of the peak to the front slope, with all measurements made at 5% of the maximum peak height. tailing_factor = Tf = W0.05/2a where W0.05 is peak width at 5% max peak height a = min width to peak maximum at 5% max peak height b = max width to peak maximum at 5% max peak height 0.9 < Tf < 1.2 front Tf < 0.9 tailing Tf > 1.2
slope_of_baseline	The slope of the baseline is a measure of slope change. It is approximated as the difference in baselines between the peak start and peak end.
Convex hull	The peak’s hull points
asymmetry_factor	The asymmetry factor is a measure of peak tailing.
asymmetry_factor	The asymmetry factor is a measure of peak tailing.
asymmetry_factor	The asymmetry factor is a measure of peak tailing. It is defined as the distance from the center line of the peak to the back slope divided by the distance from the center line of the peak to the front slope, with all measurements made at 10% of the maximum peak height. asymmetry_factor = As = b/a where a is min width to peak maximum at 10% max peak height b is max width to peak maximum at 10% max peak height
baseline_delta_2_height	The change in baseline divided by the height is a way of comparing the influence of the change of baseline on the peak height.
calculated_concentration	The absolute concentration of the component determined by applying a quantitation method to transform the measured peak area or height to concentration.
logSN	Log10 of the signal to noise ratio.
peak_apex_int	The peak’s highest intensity
peak_area	The peak’s computed area
points_across_baseline	The number of points across the baseline.
points_across_half_height	The number of points across half the peak’s height.
QC_transition_pass	True or False depending on whether the transition passed the user defined QC metrics.
QC_transition_message	The failing transition QC metrics.
QC_transition_score	The total score of all passing transition QC metrics
QC_transition_group_pass	True or False depending on whether the transition group passed the user defined QC metrics.
QC_transition_group_message	The failing transition group QC metrics.
QC_transition_group_score	The total score of all passing transition group QC metrics
total_width	The peak’s total width.
width_at_50	The width of the peak at 50% the peak’s height.
RT	The position of the point with highest intensity.
leftWidth	The time or mass to charge of the left end of the peak.
rightWidth	the time or mass to charge of the right end of the peak.
scan_polarity	The polarity of the instrument (i.e., positive or negative for electrospray ionization)
description	The description of the component.
modifications	Adducts that were measured in addition to the component.
chemical_formula	The predicted chemical formula for the component.
mz	The mass to charge ratio.
charge	The charge of the component.
mz_error_ppm	The difference between measured and predicted mass to charge ratio error in parts per million.
mz_error_Da	The difference between measured and predicted mass to charge ratio error in Daltons
average_accuracy	todo
absolute_difference	todo

What do the integrity checks do?

The integrity checks allow the user to check that the input files are consistent prior to executing a workflow.

Integrity checks

Type	Description
SAMPLE	Are sample names consistent between the Sequence and StandardsConcentrations files?
COMP	Are the component_names consistent between the Transitions, QuantitationMethods, StandardsConcentrations, FeatureFilters, and FeatureQCs files?
COMP_GROUP	Are the component_group_names consistent between the Transitions, FeatureFilters, and FeatureQCs files?
IS	Is the same internal standard (IS) specified for the same component in the QuantitationMethods and StandardsConcentrations files?

SmartPeak is slowing down the computation in time.

If SmartPeak seems to be taking more and more time for processing another data samples, it is most likely due to RAM issues. At the end of the computation workflow add CLEAR_DATA step, which clears the memory and enables its better utilization.

Where is the log file stored?

Please visit Path to logs.

My question is not listed here. How can I contact the developers?

SmartPeak is an open-source project that values feedback from the community. Please feel free to notify us of any bugs, request any features, or ask any questions by filing an Issue as https://github.com/AutoFlowResearch/SmartPeak/issues.