diff --git a/docs/about/parameters.rst b/docs/about/parameters.rst deleted file mode 100644 index 270c28f79..000000000 --- a/docs/about/parameters.rst +++ /dev/null @@ -1,279 +0,0 @@ -SmartPeak Parameters -==================== - -This page describes SmartPeak parameters, options and names. - -.. _sample-types: - -Sample Types ------------- - -.. list-table:: - :widths: 25 75 - :header-rows: 1 - - * - Type - - Description - * - Unknown - - todo - * - Standard - - todo - * - QC - - todo - * - Blank - - todo - * - Double Blank - - todo - * - Solvent - - todo - * - Unrecognized - - todo - -.. _metadata: - -Metadata --------- - -.. list-table:: - :widths: 25 75 - :header-rows: 1 - - * - 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: - -Workflow Commands ------------------ - -Raw Data Methods -~~~~~~~~~~~~~~~~ - -.. list-table:: - :widths: 25 75 - :header-rows: 1 - - * - 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 -~~~~~~~~~~~~~~~~~~~~~~~~ - -.. list-table:: - :widths: 25 75 - :header-rows: 1 - - * - 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 -~~~~~~~~~~~~~~~~~~~~ - -.. list-table:: - :widths: 25 75 - :header-rows: 1 - - * - 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: - -Integrity Checks ----------------- - -.. list-table:: - :widths: 25 75 - :header-rows: 1 - - * - Type - - Description - * - SAMPLE - - todo - * - COMP - - todo - * - COMP_GROUP - - todo - * - IS - - todo - \ No newline at end of file diff --git a/docs/faq.rst b/docs/faq.rst deleted file mode 100644 index 9dbcf8896..000000000 --- a/docs/faq.rst +++ /dev/null @@ -1,11 +0,0 @@ -FAQ -=== - -This is a list of Frequently Asked Questions about SmartPeak. Feel free to suggest new entries! - -**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 :ref:`logs`. diff --git a/docs/guide/guistart.rst b/docs/guide/gui.rst similarity index 90% rename from docs/guide/guistart.rst rename to docs/guide/gui.rst index c7ca2587d..7b09b1ce5 100644 --- a/docs/guide/guistart.rst +++ b/docs/guide/gui.rst @@ -3,7 +3,7 @@ Using SmartPeak GUI ---------------------------------------------------------------------------------------------------------- -After successful installation of SmartPeak, on Windows open menu start and browse for relevant icon, you can also find the shortcut on desktop. +This page describes the graphical user interface (GUI) for working with SmartPeak. SmartPeak GUI provides functionality to facilitate users to get up and running as quickly as possible. SmartPeak GUI also provides various graphical views and plots to enable faster debugging and configuration of workflows and algorithms. After installation of SmartPeak on Windows, MacOS, and/or Linux, a shortcut should be available for quickly launching the application. .. _logs: diff --git a/docs/guide/install.rst b/docs/guide/install.rst index 05d8f3fc9..4e1ed8779 100644 --- a/docs/guide/install.rst +++ b/docs/guide/install.rst @@ -9,17 +9,17 @@ Example on Ubuntu .. code-block:: bash - wget https://github.com/AutoFlowResearch/SmartPeak/releases/download/v1.2.0/SmartPeak-1.2.0-Linux.deb - sudo dpkg -i SmartPeak-1.2.0-Linux.deb + wget https://github.com/AutoFlowResearch/SmartPeak/releases/download/v1.26.0/SmartPeak-1.26.0-Linux.deb + sudo dpkg -i SmartPeak-1.26.0-Linux.deb sudo apt-get install -f -User can also use GUI by double clicking on SmartPeak-1.2.0-Linux.deb icon and requesting installation through Ubuntu Software. +User can also use GUI by double clicking on SmartPeak-1.26.0-Linux.deb icon and requesting installation through Ubuntu Software. Example on Windows ------------------ -Download latest release for windows, e.g. ``SmartPeak-1.2.0-win64.exe`` and double click on the icon. +Download latest release for windows, e.g. ``SmartPeak-1.26.0-win64.exe`` and double click on the icon. The wizard will guide you through the installation process. A warning from Windows Defender SmartScreen may appear. diff --git a/docs/guide/server.rst b/docs/guide/server.rst new file mode 100644 index 000000000..f26e2e6f7 --- /dev/null +++ b/docs/guide/server.rst @@ -0,0 +1,23 @@ +.. begin_smartpeak_server_usage + +Using SmartPeak Server +---------------------------------------------------------------------------------------------------------- + +This page describes the remote server for scaling SmartPeak to large and computationally demanding workflows using high performance computing (HPC) resources. +The SmartPeak Server utilizes containerization and gRPC to enable users to connect, control, and view a remote session using the SmartPeak GUI. +An IT administrator would most likely be required to set-up the remote server on the HPC resources and ensure file transfer and security are in place. +The SmartPeak team maintains containerized versions of the SmartPeak `CLI `_ and `Server `_ on DockerHub that are required for setting up the workers and server, respectively. + +.. todo:: + Describe the functionality of the SmartPeak Server. + +.. todo:: + Describe how to set-up the SmartPeak Server as an IT administrator. + +.. todo:: + Describe how to connect to the SmartPeak Server as a user. + +.. warning:: + SmartPeak Server is currently experimental! + +.. end_smartpeak_server_usage \ No newline at end of file diff --git a/docs/guide/tutorials.rst b/docs/guide/tutorials.rst index 2c2553c75..7b2d6d223 100644 --- a/docs/guide/tutorials.rst +++ b/docs/guide/tutorials.rst @@ -1,13 +1,20 @@ Tutorials & Demos ============================================================================= -This section covers a breadth of walkthroughs using different datasets and analytical techniques. +This section covers a breadth of walkthroughs using different datasets and analytical techniques. +All of the datasets used in the tutorials can be found on `GitHub `_. +The datasets and input files can be used as templates for getting started with a new and similar workflow in SmartPeak. +* :doc:`tutorials/Targeted_quantitation_with_LC-MSMS_5500_QTRAP_RapidRIP`. * :doc:`tutorials/Targeted_quantitation_with_HPLC_data`. * :doc:`tutorials/Non-targeted_FIA-MS_analysis_with_Thermo_Orbitrap`. +* :doc:`tutorials/Non-targeted_LC-MSMS_DDA_analysis_with_Thermo_Orbitrap`. + +* :doc:`tutorials/Non-targeted_LC-MSMS_DIA_analysis`. + * :doc:`tutorials/Targeted_flux_analysis_with_LC-MSMS_Agilent_Lipidomics`. * :doc:`tutorials/Targeted_flux_analysis_with_GC-MS_SIM_Agilent`. diff --git a/docs/guide/tutorials/Non-targeted_FIA-MS_analysis_with_Thermo_Orbitrap.rst b/docs/guide/tutorials/Non-targeted_FIA-MS_analysis_with_Thermo_Orbitrap.rst index 66b0f231c..609fce7b6 100644 --- a/docs/guide/tutorials/Non-targeted_FIA-MS_analysis_with_Thermo_Orbitrap.rst +++ b/docs/guide/tutorials/Non-targeted_FIA-MS_analysis_with_Thermo_Orbitrap.rst @@ -1,9 +1,11 @@ -Non-targeted FIA-MS analysis with Thermo Orbitrap +Non-targeted analysis using FIA-MS acquisition ------------------------------------------------- This tutorial walks you through the workflow for analyzing non-targeted FIA-MS data starting from input file generation, to processing the data in SmartPeak, -to reviewing the data in SmartPeak, to reporting the results for later use. +to reviewing the data in SmartPeak, to reporting the results. + +.. image:: ../../images/MassSpecSchemas-FIAMS.png Objectives ~~~~~~~~~~ @@ -19,6 +21,12 @@ The Workflows include #. Processing Unknowns #. Reviewing the results +Notes +~~~~~ + +The algorithm parameters used in the following workflows have been highly tuned for feature detection using the Thermo Orbitrap technology. +Slight modifications to the algorithm parameters in the ``FIAMS``, ``Pick2DFeatures``, and ``AccurateMassSearchEngine`` sections are needed for Time of Flight (ToF) technologies. + Steps ~~~~~ @@ -73,36 +81,48 @@ added or deleted direclty from SmartPeakGUI within the "workflow" tap in the rig A detailed explanation of each command step can be found in :ref:`Workflow Commands`. - * LOAD_RAW_DATA - * EXTRACT_SPECTRA_WINDOWS - * MERGE_SPECTRA - * PICK_MS1_FEATURES - * SEARCH_ACCURATE_MASS - * STORE_ANNOTATIONS - * STORE_FEATURES - * ESTIMATE_FEATURE_BACKGROUND_INTERFERENCES - * STORE_FEATURE_BACKGROUND_ESTIMATIONS - * FILTER_FEATURES_BACKGROUND_INTERFERENCES - * MERGE_FEATURES - * MERGE_INJECTIONS - * STORE_FEATURES_SAMPLE_GROUP + .. list-table:: workflow_FIAMS_Unknowns.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - EXTRACT_SPECTRA_WINDOWS + * - MERGE_SPECTRA + * - PICK_MS1_FEATURES + * - SEARCH_ACCURATE_MASS + * - STORE_ANNOTATIONS + * - STORE_FEATURES + * - ESTIMATE_FEATURE_BACKGROUND_INTERFERENCES + * - STORE_FEATURE_BACKGROUND_ESTIMATIONS + * - FILTER_FEATURES_BACKGROUND_INTERFERENCES + * - MERGE_FEATURES + * - MERGE_INJECTIONS + * - STORE_FEATURES_SAMPLE_GROUP The workflow pipeline is initialized by loading the raw data followed by extracting the spectra windows based on the given parameters by the user then merging spectras over the time axis. Once done, the peak picking routine will be executed on the MS1 spectras followed by executing the mass search routine. As an intermediate workflow step, the mzTab annotations and feature lists are saved - to disk as ``mzTab`` and ``featureXML`` file formats respectively. A major processing - step in this workflow is to estimate the Background Interferences for component and - component group feature filter as well as ion intensity attributes from blank samples - followed by storing component and component group percent Background Interference - estimations to disk. Then, filter transitions and transitions groups based on criteria - provided by the user followed by creating merged features from the accurate mass search - results as well as merging multiple injections of the same sample. An as the final step - in the workflow pipeline, the features for the sample group is saved to disk as a + to disk as ``mzTab`` and ``featureXML`` file formats respectively. + The feature list can be saved before or after the features are annotated using the mass search routine + depending upon whether a user would like to re-process the feature list using different accurate + mass search databases. Options are included for retaining or removing features that were not annotated. + + A major processing step in this workflow is to estimate the Background Interferences + for component features from blank samples. + Blank samples in the ``same sequence_segment`` are used to estimate the average Background Intereference for each user specified component. + The Background Intereference Estimates are saved to disk for inspection and re-use. + Then, components can be filtered based on their percentage signal intensity found in the blanks and specified by the user. + + Another major processing step in the workflow is the merging of features and injections. + Adducts corresponding to the same compound are merged into a single feature. + Injections corresponding to a single sample are merged into a single sample. + The user can specify which injections correspond to which sample group using the ``sample_group_name`` column in the ``sequence`` file. + In addition, the user can specify how features and/or injections are merged in the ``parameters`` file. + Finally, features for the sample group (i.e., merged injections) are saved to disk as a ``featureXML`` file. - The Spectra for the two injection samples can be inspected after all workflow steps had been run, to do so please click on view and then "Spectra". From the Injections tab check "Plot/Unplot All" select all injection samples and plot the mass to charge ratio relative to their respective intensities as shown below: @@ -131,4 +151,4 @@ can be found in :ref:`Workflow Commands`. data for a given injection sample which includes a list of features with a set of ``UserParam`` for each feature such as ``PeptideRef``, ``native_id`` and ``scan_polarity``. The ``mzTab`` file includes a summary of the accurate mass search. These files can be parsed and processed by the `pyOpenMS `_ - Python package. + Python package. Examples of FIA-MS post-processing analyses can be found in `BFAIR `_. diff --git a/docs/guide/tutorials/Non-targeted_LC-MSMS_DDA_analysis_with_Thermo_Orbitrap.rst b/docs/guide/tutorials/Non-targeted_LC-MSMS_DDA_analysis_with_Thermo_Orbitrap.rst index 8b8cc38af..89ed1a64a 100644 --- a/docs/guide/tutorials/Non-targeted_LC-MSMS_DDA_analysis_with_Thermo_Orbitrap.rst +++ b/docs/guide/tutorials/Non-targeted_LC-MSMS_DDA_analysis_with_Thermo_Orbitrap.rst @@ -1,2 +1,207 @@ -Non-targeted LC-MS/MS DDA analysis with Thermo Orbitrap -------------------------------------------------------- \ No newline at end of file +Non-targeted analysis using LC-MS/MS DDA acquisition +---------------------------------------------------- + +This tutorial walks you through the workflow for analyzing non-targeted liquid chromatography high resolution mass spectrometry (LC-MS/MS) data-dependent acquisition (DDA) +data starting from input file generation, to processing the data in SmartPeak, +to reviewing the data in SmartPeak, to reporting the results. + +.. image:: ../../images/MassSpecSchemas-DDA.png + +Objectives +~~~~~~~~~~ + +#. Obtaining the SOP for the workflow. +#. Choosing a data set for demonstrating the workflow. +#. Creating an optimized SmartPeak input templates for running the workflow. + +The Workflows include +~~~~~~~~~~~~~~~~~~~~~ + +#. Defining the accurate mass search database +#. Processing Unknowns based MS1 accurate mass and creating a transition library based on MS2 product ion scans +#. Processing Unknowns based MS1 accurate mass and creating a spectral database based on MS2 product ion scans +#. Processing Unknowns based on MS2 product ion scans using an existing spectral database +#. Reviewing the results + +Notes +~~~~~ + +The algorithm parameters used in the following workflows have been highly tuned for feature detection using Time of Flight (Tof) technologies. +Slight modifications to the algorithm parameters in the ``TargetedSpectraExtractor`` section is needed for Orbitrap technology and other acquisition method specific parameters. + +Steps +~~~~~ + +The tutorial includes the following steps : + +#. Setting up the input files + + The data set used can be found in + `LC-MS/MS-DDA `_ + for the transition library and spectral database generation, and spectral library matching workflows. + + The dataset includes a ``CHEMISTRY`` folder which contains HMDB (Human Metabolome Database) mapping files organized as follows: + + #. HMDB2StructMapping.tsv + + This tab seperated file contains mapping of HMDB IDs, IUPAC Name, Compound Summary (Synonyms), Canonical SMILES and InChl. + + #. HMDBMappingFile.tsv + + This tab seperated file contains the Monoisotopic Molecular Weight and the Chemical Formula mapped to their respective HMDB ID. + + #. negative_adducts.tsv + + This file contains negative ion modes including the charge. + + #. positive_adducts.tsv + + This file contains positive ion modes including the charge. + + The above files provided in the example are appropriate for applications involving human serum and other biosamples. For applications involving other organisms such as bacteria (e.g., E. coli), the use of organism specific databases are recommended to reduce the number of false positives. + See `FIA_MS_database_construction.ipynb `_ for an example notebook demonstrating how to convert the metabolites in a genome-scale reconstruction to SmartPeak accurate mass mapping files. + + Furthermore, the ``parameters.csv`` file contains the following settings for this workflow: + + .. table:: DDA_parameters.csv + :widths: auto + + ======================== ================================================= =============================================== ====== + function name value type + ======================== ================================================= =============================================== ====== + FeatureFindingMetabo report_chromatograms TRUE bool + FeatureFindingMetabo report_convex_hulls TRUE bool + FeatureFindingMetabo use_smoothed_intensities FALSE bool + Pick3DFeatures enable_elution FALSE bool + Pick3DFeatures max_traces 1000 int + Pick3DFeatures force_processing FALSE bool + TargetedSpectraExtractor AccurateMassSearchEngine:db:mapping ['CHEMISTRY/HMDBMappingFileGermicidinA.tsv'] list + TargetedSpectraExtractor AccurateMassSearchEngine:db:struct ['CHEMISTRY/HMDB2StructMappingGermicidinA.tsv'] list + TargetedSpectraExtractor AccurateMassSearchEngine:positive_adducts CHEMISTRY/PositiveAdducts.tsv string + TargetedSpectraExtractor AccurateMassSearchEngine:negative_adducts CHEMISTRY/NegativeAdducts.tsv string + TargetedSpectraExtractor relative_allowable_product_mass 50 float + TargetedSpectraExtractor AccurateMassSearchEngine:ionization_mode auto string + TargetedSpectraExtractor AccurateMassSearchEngine:mass_error_value 10 float + TargetedSpectraExtractor rt_window 60 float + TargetedSpectraExtractor mz_tolerance 0.001 float + TargetedSpectraExtractor AccurateMassSearchEngine:keep_unidentified_masses TRUE bool + ======================== ================================================= =============================================== ====== + +#. Defining the workflow in SmartPeak + +For LC-MS/MS-DDA transition library generation analysis, the following steps are saved into the ``workflow.csv`` file. +Alternatively, steps can be replaced, added or deleted direclty from SmartPeakGUI. +A detailed explanation of each command step can be found in :ref:`Workflow Commands`. + + .. list-table:: workflow_LCMS_DDA_transition.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - PICK_3D_FEATURES + * - SEARCH_SPECTRUM_MS1 + * - MERGE_FEATURES_MS1 + * - EXTRACT_SPECTRA_NON_TARGETED + * - SEARCH_SPECTRUM_MS2 + * - MERGE_FEATURES_MS2 + * - CONSTRUCT_TRANSITIONS_LIST + * - STORE_FEATURES + + The workflow process's data dependent acquisition (DDA) data generated by liquid chromatography mass spectrometry instrumentation. + + The workflow first picks, annotates, and merges features found in the MS1 scans for each sample, second picks, annotates, and merges features found in the MS2 scans for each sample, and third constructs a transition list for downstream quantification using e.g., data independent acquisition (DIA) or single reaction monitoring (SRM) methods. + + The transition library generated for each sample can be found in the ``output features`` directory. A snippet of the table is shown below. + + .. table:: DDA_transition_library.csv + :widths: auto + + =========== =========== =============== ============= ================ ======================= ================ ================= ========================================= + PrecursorMz ProductMz PrecursorCharge ProductCharge LibraryIntensity NormalizedRetentionTime ProteinId TransitionGroupId TransitionId + =========== =========== =============== ============= ================ ======================= ================ ================= ========================================= + 235.0747741 134.9568506 0 NA 476 329.3195788 HMDB:HMDB0000001 HMDB:HMDB0000001 HMDB:HMDB0000001_scan=440_134.957_370.346 + 235.0747741 217.1050819 0 NA 464 329.3195788 HMDB:HMDB0000001 HMDB:HMDB0000001 HMDB:HMDB0000001_scan=440_217.105_370.346 + =========== =========== =============== ============= ================ ======================= ================ ================= ========================================= + + Statistics on each of the individual scans analyzed can be viewed at ``view | scans``. + + .. image:: ../../images/lcms_dda_scans_table.png + + The features found can be viewed at ``view | features (table)`` in long form. + + .. image:: ../../images/lcms_dda_features_table.png + + Or at ``view | features (matrix)`` in compact form. + + .. image:: ../../images/lcms_dda_features_matrix.png + + The TIC for each injection can be viewed at ``view | chromatograms``. + + .. image:: ../../images/lcms_dda_tic_chromatogram.png + + Clicking on the chromatogram reveals the MS1 spectra acquired at the selected time-point. + + .. image:: ../../images/lcms_dda_tic_spectra.png + + Clicking on the spectra computes and displays the MS1 XIC for the selected m/z. + + .. image:: ../../images/lcms_dda_xic_chromatogram.png + + Clicking on the MS1 XIC chromatogram revealse the MS2 spectra acquired at the selected time-point. + + .. image:: ../../images/lcms_dda_xic_spectra.png + +#. Defining the workflow in SmartPeak + +For LC-MS/MS-DDA spectral database generation analysis, the following steps are saved into the ``workflow.csv`` file. +Alternatively, steps can be replaced, added or deleted direclty from SmartPeakGUI. +A detailed explanation of each command step can be found in :ref:`Workflow Commands`. + + .. list-table:: workflow_LCMS_DDA_spectral.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - PICK_3D_FEATURES + * - SEARCH_SPECTRUM_MS1 + * - MERGE_FEATURES_MS1 + * - EXTRACT_SPECTRA_NON_TARGETED + * - STORE_MSP + * - STORE_FEATURES + + The workflow process's data dependent acquisition (DDA) data generated by liquid chromatography mass spectrometry instrumentation. + + The workflow first picks, annotates, and merges features found in the MS1 scans for each sample, second picks features found in the MS2 scans for each sample, and third constructs a spectral library for downstream spectral annotation. + + The spectral database in MSP format generated for each sample can be found in the ``output features`` directory. A snippet of the table is shown below. + + .. list-table:: DDA_spectral_library.csv + :header-rows: 0 + + * - Name: HMDB:HMDB0000001 + * - Retention Time: 370.346 + * - base peak intensity: 476.0 + * - total ion current: 940.0 + * - Num Peaks: 2 + * - 134.957:476 217.105:464 + +#. Defining the workflow in SmartPeak + +For LC-MS/MS-DDA spectral database matching analysis, the following steps are saved into the ``workflow.csv`` file. +Alternatively, steps can be replaced, added or deleted direclty from SmartPeakGUI. +A detailed explanation of each command step can be found in :ref:`Workflow Commands`. + + .. list-table:: workflow_LCMS_DDA_spectra.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - PICK_3D_FEATURES + * - EXTRACT_SPECTRA_NON_TARGETED + * - MATCH_SPECTRA + * - STORE_FEATURES + + The workflow process's data dependent acquisition (DDA) data generated by liquid chromatography mass spectrometry instrumentation. + + The workflow first picks features found in the MS1 scans for each sample, second picks features found in the MS2 scans for each sample, and third annotates the MS1 features by matching the spectra of the MS2 scans with a spectral library. + diff --git a/docs/guide/tutorials/Non-targeted_LC-MSMS_DIA_analysis.rst b/docs/guide/tutorials/Non-targeted_LC-MSMS_DIA_analysis.rst new file mode 100644 index 000000000..ce88c714e --- /dev/null +++ b/docs/guide/tutorials/Non-targeted_LC-MSMS_DIA_analysis.rst @@ -0,0 +1,28 @@ +Non-targeted analysis using LC-MS/MS DIA acquisition +---------------------------------------------------- + +This tutorial walks you through the workflow for analyzing non-targeted liquid chromatography high resolution mass spectrometry (LC-MS/MS) data-independent acquisition (DIA) +data starting from input file generation, to processing the data in SmartPeak, +to reviewing the data in SmartPeak, to reporting the results. + +.. image:: ../../images/MassSpecSchemas-DIA.png + +Objectives +~~~~~~~~~~ + +#. Obtaining the SOP for the workflow. +#. Choosing a data set for demonstrating the workflow. +#. Creating an optimized SmartPeak input templates for running the workflow. + +The Workflows include +~~~~~~~~~~~~~~~~~~~~~ + +#. Defining the transition library +#. Processing Unknowns +#. Reviewing the results + +.. todo:: + The rest of the tutorial. + +.. warning:: + SmartPeak supports metabolomics, lipidomics, and proteomics DIA workflows. Please contact us if you are interested in including your dataset as an example. diff --git a/docs/guide/tutorials/Targeted_flux_analysis_with_GC-MS_SIM_Agilent.rst b/docs/guide/tutorials/Targeted_flux_analysis_with_GC-MS_SIM_Agilent.rst index bebffe325..110808d76 100644 --- a/docs/guide/tutorials/Targeted_flux_analysis_with_GC-MS_SIM_Agilent.rst +++ b/docs/guide/tutorials/Targeted_flux_analysis_with_GC-MS_SIM_Agilent.rst @@ -1,10 +1,12 @@ -Targeted flux analysis with GC-MS SIM Agilent ---------------------------------------------- +Targeted flux analysis using GC-MS SIM acquisition +-------------------------------------------------- This tutorial walks you through the workflow for analyzing targeted flux analysis using SIM GC-MS/MS data starting from input file generation, to processing the data in SmartPeak, to reviewing the data in SmartPeak, to reporting the results for later use. +.. image:: ../../images/MassSpecSchemas-GCMSSIM.png + Objectives ~~~~~~~~~~ @@ -18,6 +20,12 @@ The Workflows include #. Processing Unknowns #. Reviewing the results +Notes +~~~~~ + +The algorithm parameters used in the following workflows have been highly tuned for feature detection using an Agilent GC and single quad system. +With that said, we have found the algorithm parameters to generalize well to most gas chromatography coupled to mass spectrometry systems. + Steps ~~~~~ @@ -41,18 +49,22 @@ added or deleted direclty from SmartPeakGUI within the "workflow" tap in the rig A detailed explanation of each command step can be found in :ref:`Workflow Commands`. - * LOAD_RAW_DATA - * MAP_CHROMATOGRAMS - * EXTRACT_CHROMATOGRAM_WINDOWS - * ZERO_CHROMATOGRAM_BASELINE - * PICK_MRM_FEATURES - * QUANTIFY_FEATURES - * CHECK_FEATURES - * SELECT_FEATURES - * CALCULATE_MDVS - * ISOTOPIC_CORRECTIONS - * CALCULATE_MDV_ACCURACIES - * STORE_FEATURES + .. list-table:: workflow_GCMSSIM_Flux_Unknowns.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - MAP_CHROMATOGRAMS + * - EXTRACT_CHROMATOGRAM_WINDOWS + * - ZERO_CHROMATOGRAM_BASELINE + * - PICK_MRM_FEATURES + * - QUANTIFY_FEATURES + * - CHECK_FEATURES + * - SELECT_FEATURES + * - CALCULATE_MDVS + * - ISOTOPIC_CORRECTIONS + * - CALCULATE_MDV_ACCURACIES + * - STORE_FEATURES The workflow pipeline is initialized by loading the raw data followed by mapping the chromatograms to the loaded set of transitions. Once done, @@ -65,7 +77,7 @@ can be found in :ref:`Workflow Commands`. alignment algorithms is executed. Mass distribution vectors can then be calculated followed by isotopic corrections and comparing the MDVs to the theoretical values. As the final step in the workflow, the features - for the sample group is stored to disk as a ``featureXML`` files. + for the sample group is stored to disk as a ``featureXML`` files. To plot the intensities over time for given injections and transitions, view the "chromatogram" from the "view" menu then select the injections and transitions to plot from their respective tabs on the left. The following shows the chromatogram @@ -78,10 +90,10 @@ can be found in :ref:`Workflow Commands`. .. image:: ../../images/gcms_sim_unknowns_heatmap.png - #. Reporting the results +#. Reporting the results - To export the results, select "Report" from the "Actions" which will show the - "Create Report" window: +To export the results, select "Report" from the "Actions" which will show the +"Create Report" window: .. image:: ../../images/lcms_targeted_flux_exports.png diff --git a/docs/guide/tutorials/Targeted_flux_analysis_with_GC-MS_full-scan_Agilent.rst b/docs/guide/tutorials/Targeted_flux_analysis_with_GC-MS_full-scan_Agilent.rst index be3cc7a25..6ac7d64b8 100644 --- a/docs/guide/tutorials/Targeted_flux_analysis_with_GC-MS_full-scan_Agilent.rst +++ b/docs/guide/tutorials/Targeted_flux_analysis_with_GC-MS_full-scan_Agilent.rst @@ -1,9 +1,11 @@ -Targeted flux analysis with GC-MS full-scan Agilent ---------------------------------------------------- +Targeted flux analysis using GC-MS full-scan acquisition +-------------------------------------------------------- This tutorial walks you through the workflow for analyzing targeted full-scan flux analysis using SIM GC-MS data starting from input file generation, to processing the data in SmartPeak, -to reviewing the data in SmartPeak, to reporting the results for later use. +to reviewing the data in SmartPeak, to reporting the results. + +.. image:: ../../images/MassSpecSchemas-GCMSFullScan.png Objectives ~~~~~~~~~~ @@ -18,6 +20,12 @@ The Workflows include #. Processing Unknowns #. Reviewing the results +Notes +~~~~~ + +The algorithm parameters used in the following workflows have been highly tuned for feature detection using an Agilent GC and single quad system. +With that said, we have found the algorithm parameters to generalize well to most gas chromatography coupled to mass spectrometry systems. + Steps ~~~~~ @@ -41,18 +49,22 @@ added or deleted direclty from SmartPeakGUI within the "workflow" tap in the rig A detailed explanation of each command step can be found in :ref:`Workflow Commands`. - * LOAD_RAW_DATA - * MAP_CHROMATOGRAMS - * EXTRACT_CHROMATOGRAM_WINDOWS - * ZERO_CHROMATOGRAM_BASELINE - * PICK_MRM_FEATURES - * QUANTIFY_FEATURES - * CHECK_FEATURES - * SELECT_FEATURES - * CALCULATE_MDVS - * ISOTOPIC_CORRECTIONS - * CALCULATE_MDV_ACCURACIES - * STORE_FEATURES + .. list-table:: workflow_GCMSFullScan_Flux_Unknowns.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - MAP_CHROMATOGRAMS + * - EXTRACT_CHROMATOGRAM_WINDOWS + * - ZERO_CHROMATOGRAM_BASELINE + * - PICK_MRM_FEATURES + * - QUANTIFY_FEATURES + * - CHECK_FEATURES + * - SELECT_FEATURES + * - CALCULATE_MDVS + * - ISOTOPIC_CORRECTIONS + * - CALCULATE_MDV_ACCURACIES + * - STORE_FEATURES The workflow pipeline is initialized by loading the raw data followed by mapping the chromatograms to the loaded set of transitions. Once done, @@ -65,7 +77,7 @@ can be found in :ref:`Workflow Commands`. alignment algorithms is executed. Mass distribution vectors can then be calculated followed by isotopic corrections and comparing the MDVs to the theoretical values. As the final step in the workflow, the features - for the sample group is stored to disk as a ``featureXML`` files. + for the sample group is stored to disk as a ``featureXML`` files. To plot the intensities over time for given injections and transitions, view the "chromatogram" from the "view" menu then select the injections and transitions to plot from their respective tabs on the left. The following shows the @@ -78,7 +90,7 @@ can be found in :ref:`Workflow Commands`. .. image:: ../../images/gcms_fullscan_agilent_heapmap.png - #. Reporting the results +#. Reporting the results To export the results, select "Report" from the "Actions" which will show the "Create Report" window: diff --git a/docs/guide/tutorials/Targeted_flux_analysis_with_LC-MSMS_Agilent_Lipidomics.rst b/docs/guide/tutorials/Targeted_flux_analysis_with_LC-MSMS_Agilent_Lipidomics.rst index 5fda73850..118509f85 100644 --- a/docs/guide/tutorials/Targeted_flux_analysis_with_LC-MSMS_Agilent_Lipidomics.rst +++ b/docs/guide/tutorials/Targeted_flux_analysis_with_LC-MSMS_Agilent_Lipidomics.rst @@ -1,9 +1,11 @@ -Targeted flux analysis with LC-MS/MS Agilent Lipidomics -------------------------------------------------------- +Targeted flux analysis using LC-MS/MS-SRM acquisition +----------------------------------------------------- This tutorial walks you through the workflow for analyzing targeted flux analysis using LC-MS/MS data starting from input file generation, to processing the data in SmartPeak, -to reviewing the data in SmartPeak, to reporting the results for later use. +to reviewing the data in SmartPeak, to reporting the results. + +.. image:: ../../images/MassSpecSchemas-SRM.png Objectives ~~~~~~~~~~ @@ -18,6 +20,12 @@ The Workflows include #. Processing Unknowns #. Reviewing the results +Notes +~~~~~ + +The algorithm parameters used in the following workflows have been highly tuned for feature detection using tan Agilent HPLC and triple quad systems. +With that said, we have found the algorithm parameters to generalize well to most liquid chromatography coupled to mass spectrometry systems. + Steps ~~~~~ @@ -41,12 +49,16 @@ added or deleted direclty from SmartPeakGUI within the "workflow" tap in the rig A detailed explanation of each command step can be found in :ref:`Workflow Commands`. - * LOAD_RAW_DATA - * MAP_CHROMATOGRAMS - * PICK_MRM_FEATURES - * FILTER_FEATURES - * CHECK_FEATURES - * STORE_FEATURES + .. list-table:: workflow_LCMS_Flux_Unknowns.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - MAP_CHROMATOGRAMS + * - PICK_MRM_FEATURES + * - FILTER_FEATURES + * - CHECK_FEATURES + * - STORE_FEATURES The workflow pipeline is initialized by loading the raw data followed by mapping the chromatograms to the loaded set og transitions. Once done, the peak picking routine @@ -59,7 +71,7 @@ can be found in :ref:`Workflow Commands`. then select the injections and transitions to plot from their respective tabs on the left. The following shows the chromatogram for one injection using 6pgc and 23dpg transitions and their intensity differences over time. - .. image:: ../images/lcms_targeted_chromatogram.png + .. image:: ../images/lcms_targeted_flux_chromatogram.png The Spectra for the two injection samples can be inspected after all workflow steps had been run, to do so please click on view and then "Spectra". From the Injections tab check "Plot/Unplot All" select all injection samples and diff --git a/docs/guide/tutorials/Targeted_quantitation_with_HPLC_data.rst b/docs/guide/tutorials/Targeted_quantitation_with_HPLC_data.rst index 6f9a1b048..978411601 100644 --- a/docs/guide/tutorials/Targeted_quantitation_with_HPLC_data.rst +++ b/docs/guide/tutorials/Targeted_quantitation_with_HPLC_data.rst @@ -1,9 +1,11 @@ -Targeted quantitation with HPLC data ------------------------------------- +Targeted quantitation using HPLC IR and UV acquisition +------------------------------------------------------ This tutorial walks you through the workflow for analyzing targeted HPLC data starting from input file generation, to processing the data in SmartPeak, -to reviewing the data in SmartPeak, to reporting the results for later use. +to reviewing the data in SmartPeak, to reporting the results. + +.. image:: ../../images/MassSpecSchemas-HPLCUV.png Objectives ~~~~~~~~~~ @@ -15,8 +17,14 @@ Objectives The Workflows include ~~~~~~~~~~~~~~~~~~~~~ -#. Calculating the calibration curves using Standards -#. Processing Unknowns +#. Calculating the calibration curves to generate quantitation methods for each component using Standard samples +#. Processing Unknown samples using the quantitation methods + +Notes +~~~~~ + +Due to the non-standard formats used by HPLC and GC vendors, customized raw data file parsing routines are needed. +Currently, Thermo HPLC text file inputs are supported. Additional vendor input files can be supported upon request. Steps ~~~~~ @@ -38,19 +46,23 @@ added or deleted direclty from SmartPeakGUI. A detailed explanation of each command step can be found in :ref:`Workflow Commands`. - * LOAD_RAW_DATA - * MAP_CHROMATOGRAMS - * EXTRACT_CHROMATOGRAM_WINDOWS - * ZERO_CHROMATOGRAM_BASELINE - * PICK_MRM_FEATURES - * CHECK_FEATURES - * SELECT_FEATURES - * CALCULATE_CALIBRATION - * STORE_QUANTITATION_METHODS - * QUANTIFY_FEATURES - * STORE_FEATURES - - The calibration curve can be inspected after all workflow steps had been run, to do so please + .. list-table:: workflow_HPLC_UV_Standards.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - MAP_CHROMATOGRAMS + * - EXTRACT_CHROMATOGRAM_WINDOWS + * - ZERO_CHROMATOGRAM_BASELINE + * - PICK_MRM_FEATURES + * - CHECK_FEATURES + * - SELECT_FEATURES + * - CALCULATE_CALIBRATION + * - STORE_QUANTITATION_METHODS + * - QUANTIFY_FEATURES + * - STORE_FEATURES + + The calibration curve for each transition's quantitation method can be inspected after all workflow steps have been run, to do so please click on view and then "Calibrators". From the transition tab select Antranilicacid and Indole as ``transition_group`` to plot their concentration curves within the given concentration range as shown below: @@ -85,15 +97,19 @@ can be found in :ref:`Workflow Commands`. The workflow steps for HPLC UV Unknowns are : - * LOAD_RAW_DATA - * MAP_CHROMATOGRAMS - * EXTRACT_CHROMATOGRAM_WINDOWS - * ZERO_CHROMATOGRAM_BASELINE - * PICK_MRM_FEATURES - * QUANTIFY_FEATURES - * CHECK_FEATURES - * SELECT_FEATURES - * STORE_FEATURES + .. list-table:: workflow_HPLC_UV_Unknowns.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - MAP_CHROMATOGRAMS + * - EXTRACT_CHROMATOGRAM_WINDOWS + * - ZERO_CHROMATOGRAM_BASELINE + * - PICK_MRM_FEATURES + * - QUANTIFY_FEATURES + * - CHECK_FEATURES + * - SELECT_FEATURES + * - STORE_FEATURES To inspect the features for the selected transition groups, select "Features (line)" from the view menu then open the features tab (can be opened from the view menu as well) to select the "asymetry_factors" and "logSN" @@ -116,7 +132,7 @@ The workflow steps for HPLC UV Unknowns are : To run the analysis, please follow the steps for :ref:`Using SmartPeak GUI` or :ref:`Using SmartPeak CLI` - to execute the workflow steps and review the results including plotting. + to execute the workflow steps, review the results, and report the results. #. Reporting the results diff --git a/docs/guide/tutorials/Targeted_quantitation_with_LC-MSMS_5500_QTRAP_RapidRIP.rst b/docs/guide/tutorials/Targeted_quantitation_with_LC-MSMS_5500_QTRAP_RapidRIP.rst index c65bf20a6..4cb2fbd3c 100644 --- a/docs/guide/tutorials/Targeted_quantitation_with_LC-MSMS_5500_QTRAP_RapidRIP.rst +++ b/docs/guide/tutorials/Targeted_quantitation_with_LC-MSMS_5500_QTRAP_RapidRIP.rst @@ -1,2 +1,150 @@ -Targeted quantitation with LC-MS/MS 5500 QTRAP RapidRIP -------------------------------------------------------- \ No newline at end of file +Targeted quantitation using LC-MS/MS-SRM acquisition +---------------------------------------------------- + +This tutorial walks you through the workflow for analyzing targeted single reaction monitoring (SRM) data +starting from input file generation, to processing the data in SmartPeak, +to reviewing the data in SmartPeak, to reporting the results. + +.. image:: ../../images/MassSpecSchemas-SRM.png + +Objectives +~~~~~~~~~~ + +#. Obtaining the SOP for the workflow. +#. Choosing a data set for demonstrating the workflow. +#. Creating an optimized SmartPeak input templates for running the workflow. + +The Workflows include +~~~~~~~~~~~~~~~~~~~~~ + +#. Calculating the calibration curves to generate quantitation methods for each component using Standard samples +#. Processing Unknown samples using the quantitation methods + +Notes +~~~~~ + +The algorithm parameters used in the following workflows have been highly tuned for feature detection using the Sciex 5500 QTRAP and 6500+ systems with Shimadzu and Agilent HPLC systems. +With that said, we have found the algorithm parameters to generalize well to most liquid chromatography coupled to mass spectrometry systems. + +Steps +~~~~~ + +The tutorial includes the following steps : + +#. Setting up the input files + +The data set used can be found in +`LCMS_SRM_Standards `_, +`LCMS_SRM_QCs `_, and +`LCMS_SRM_Unknowns `_ +for the LC-MS/MS-SRM Standards, QCs, and Unknowns, respectively. + +#. Defining the workflow in SmartPeak + +For LC-MS/MS-SRM Standards analysis, the following steps are saved +into the ``workflow.csv`` file. Alternatively, steps can be replaced, +added or deleted direclty from SmartPeakGUI. +A detailed explanation of each command step +can be found in :ref:`Workflow Commands`. + + .. list-table:: workflow_LCMSSRM_Standards.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - MAP_CHROMATOGRAMS + * - PICK_MRM_FEATURES + * - CHECK_FEATURES + * - SELECT_FEATURES + * - CALCULATE_CALIBRATION + * - STORE_QUANTITATION_METHODS + * - QUANTIFY_FEATURES + * - STORE_FEATURES + + The calibration curve for each transition's quantitation method can be inspected after all workflow steps have been run, to do so please + click on view and then "Calibrators". From the menu select ser-L.ser-L_1.Light + as ``component`` to plot its concentration curves within the given concentration range as + shown below: + + .. image:: ../../images/calibrators.png + + To inspect the features for the selected transition groups, select "Features (line)" from the view menu + then open the features tab (can be opened from the view menu as well) to select the "asymetry_factors" and "logSN" + in the plot column. The line plot illistrates the value for each transition group and feature as shown below: + + .. image:: ../../images/lcms_srm_standards_features_line.png + + The features can also be plotted as a heatmap, under "view" select "Features (heatmap)" then select the "left_width" + feature to display transition groups as a heatmap and compare the values from the same injection as shown below: + + .. image:: ../../images/lcms_srm_standards_features_heatmap.png + + To plot the intensities over time for given injections and transitions, view the "chromatogram" from the "view" menu + then select the injections and transitions to plot from their respective tabs on the left. The following shows the chromatograms + for the calibration mix 3 (CM3) series of Standards for L-serine light and heavy transitions. + + .. image:: ../../images/lcms_srm_standards_chromatograms.png + + The workflow step ``STORE_QUANTITATION_METHODS`` writes the calibration model for each transition, an excerpt can be seen below: + + .. table:: Generated sequence1_quantitationMethods.csv + :widths: auto + + =================== =================== ============= =================== ==== ==== ====== ==== ======================= ======== ==================== =================================== ====================================== ====================================== =================================== ====================================== ====================================== =============================================== ================================ ==================================== + IS_name component_name feature_name concentration_units llod ulod lloq uloq correlation_coefficient n_points transformation_model transformation_model_param_y_weight transformation_model_param_y_datum_min transformation_model_param_y_datum_max transformation_model_param_x_weight transformation_model_param_x_datum_min transformation_model_param_x_datum_max transformation_model_param_symmetric_regression transformation_model_param_slope transformation_model_param_intercept + =================== =================== ============= =================== ==== ==== ====== ==== ======================= ======== ==================== =================================== ====================================== ====================================== =================================== ====================================== ====================================== =============================================== ================================ ==================================== + 23dpg.23dpg_1.Heavy 23dpg.23dpg_1.Light peak_apex_int ug/mL 0.0 0.0 0.0025 50.0 0.998429475730303 4 linear ln(y) -1.0e15 1.0e15 ln(x) -1.0e15 1.0e15 FALSE 0.36817238220267 2.65567855569643 + 23dpg.23dpg_1.Heavy 23dpg.23dpg_2.Light peak_apex_int ug/mL 0.0 0.0 1.0 50.0 0.996468124200467 4 linear ln(y) -1.0e15 1.0e15 ln(x) -1.0e15 1.0e15 FALSE 1.14095656824418 -0.440569296738733 + =================== =================== ============= =================== ==== ==== ====== ==== ======================= ======== ==================== =================================== ====================================== ====================================== =================================== ====================================== ====================================== =============================================== ================================ ==================================== + + This file is used to apply the predefined calibration model to each transition by running the ``QUANTIFY_FEATURES`` workflow step. + + +The workflow steps for LC-MS/MS-SRM Unknowns are : + + .. list-table:: workflow_LCMSSRM_Unknowns.csv + :header-rows: 1 + + * - workflow_step + * - LOAD_RAW_DATA + * - MAP_CHROMATOGRAMS + * - PICK_MRM_FEATURES + * - QUANTIFY_FEATURES + * - CHECK_FEATURES + * - SELECT_FEATURES + * - STORE_FEATURES + + To inspect the features for the selected transition groups, select "Features (line)" from the view menu + then open the features tab (can be opened from the view menu as well) to select the "asymetry_factors" and "logSN" + in the plot column. The line plot illistrates the value for each transition group and feature as shown below: + + .. image:: ../../images/lcms_srm_unknowns_features_line.png + + The features can also be plotted as a heatmap, under "view" select "Features (heatmap)" then select the "asymetry_factors" + feature to display transition groups as a heatmap and compare the values from the same injection as shown below: + + .. image:: ../../images/lcms_srm_unknowns_features_heatmap.png + + To plot the intensities over time for given injections and transitions, view the "chromatogram" from the "view" menu + then select the injections and transitions to plot from their respective tabs on the left. The following shows the chromatogram + for three injections for L-serine light and heavy transitions. + + .. image:: ../../images/lcms_srm_unknowns_chromatograms.png + +#. Running the workflow in SmartPeak + + To run the analysis, please follow the steps for + :ref:`Using SmartPeak GUI` or :ref:`Using SmartPeak CLI` + to execute the workflow steps, review the results, and report the results. + +#. Reporting the results + + To export the results, select "Report" from the "Actions" which will show the + "Create Report" window: + + .. image:: ../../images/lcms_srm_unknowns_exports.png + + Based in the data you wish to export, select the desired "Sample types" from the left pane + and select the "Metadata" from the right pane then click on of the buttons below to create + the report with the selected items in the csv format. More details on exporting the results can be found + in :ref:`Export report`. \ No newline at end of file diff --git a/docs/guide/usage.rst b/docs/guide/usage.rst index ec51ef174..93853c57d 100644 --- a/docs/guide/usage.rst +++ b/docs/guide/usage.rst @@ -5,13 +5,16 @@ SmartPeak comes in different flavors to satisfy users' needs. The SmartPeakGUI i easy-to-use graphical user interface, advanced plotting capabilities and session saving and restoring, while the commandline version offers fast and easy to use data processing from a PC or a remote server with abundant computational resources. For larger data processing piplines, SmartPeak Team is offering a light weight yet powerful SmartPeakServer which can be deployed -to a HPC cluster to perform larger computations and connected remotely to SmartPeakGUI for a seamless user experience (Coming Soon). +to a HPC cluster to perform larger computations and connected remotely to SmartPeakGUI for a seamless user experience. -.. include:: guistart.rst +.. include:: gui.rst :start-after: begin_smartpeak_gui_usage :end-before: end_smartpeak_gui_usage - .. include:: cli.rst :start-after: begin_smartpeak_cli_usage :end-before: end_smartpeak_cli_usage + +.. include:: server.rst + :start-after: begin_smartpeak_server_usage + :end-before: end_smartpeak_server_usage diff --git a/docs/index.rst b/docs/index.rst index 90aa49ceb..5d542ca98 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -11,7 +11,7 @@ SmartPeak start/start start/features changelog - faq + start/faq .. toctree:: :caption: Step-by-step guides @@ -27,7 +27,6 @@ SmartPeak :maxdepth: 1 about/contribute - about/parameters about/developer api/library_root about/roadmap diff --git a/docs/start/faq.rst b/docs/start/faq.rst new file mode 100644 index 000000000..9871b5357 --- /dev/null +++ b/docs/start/faq.rst @@ -0,0 +1,405 @@ +FAQ +=== + +This is a list of Frequently Asked Questions about SmartPeak. + +.. _sample-types + +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. + +.. image:: ../images/MassSpecSchemas-01.png + +An example of a sequence for a bracketed experimental design common to targeted quantification experiments is provided below. + +Bracketed sequence +~~~~~~~~~~~~~~~~~~ + +.. list-table:: + :widths: 25 75 + :header-rows: 1 + + * - sample_name + - sample_type + - sample_group_name + - sequence_segment + * - blank-1 + - Blank + - blank-1 + - segment-1 + * - standard-1-low + - Standard + - standard-1 + - segment-1 + * - standard-1-medium + - Standard + - standard-1 + - segment-1 + * - standard-1-high + - Standard + - standard-1 + - segment-1 + * - sample-1-rep-1 + - Unknown + - sample-1 + - segment-1 + * - sample-1-rep-2 + - Unknown + - sample-1 + - segment-1 + * - sample-1-rep-3 + - Unknown + - sample-1 + - segment-1 + * - blank-1 + - Blank + - blank-1 + - segment-1 + * - standard-2-low + - Standard + - standard-2 + - segment-1 + * - standard-2-medium + - Standard + - standard-2 + - segment-1 + * - standard-2-high + - Standard + - standard-1 + - segment-1 + +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 +~~~~~~~~~~~~ + +.. list-table:: + :widths: 25 75 + :header-rows: 1 + + * - 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. + +.. _workflow-commands: + +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 +~~~~~~~~~~~~~~~~ + +.. list-table:: + :widths: 25 75 + :header-rows: 1 + + * - 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 +~~~~~~~~~~~~~~~~~~~~~~~~ + +.. list-table:: + :widths: 25 75 + :header-rows: 1 + + * - 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 +~~~~~~~~~~~~~~~~~~~~ + +.. list-table:: + :widths: 25 75 + :header-rows: 1 + + * - 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. + +.. _metadata: + +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 +~~~~~~~~~~~~~~~~ + +.. list-table:: + :widths: 25 75 + :header-rows: 1 + + * - 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 + +.. _integrity-checks: + +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 +~~~~~~~~~~~~~~~~ + +.. list-table:: + :widths: 25 75 + :header-rows: 1 + + * - 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? + +.. _clear-data: + +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. + +.. _log-file: + +Where is the log file stored? +----------------------------- + +Please visit :ref:`logs`. + +.. _issues: + +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. diff --git a/docs/start/features.rst b/docs/start/features.rst index 552b8a7ad..9b907cf6a 100644 --- a/docs/start/features.rst +++ b/docs/start/features.rst @@ -1,13 +1,175 @@ SmartPeak Features ============================================================================= -Select features from dilutions preference +SmartPeak provides a plethora of features for analytical chemistry data processing. An incomplete set of features are described below. + +Audit trail and data provenance +----------------------------------------------------------------------------- + +A complete record of all actions and data processing steps invoked by the user is often required in regulated environments. In addition, for debugging, it is useful to have a record of all actions the software has taken. + +SmartPeak records all actions and data processing steps for audit trail and debugging purposes at two levels: 1) an application log, and 2) feature log. + +**Application log** +The application log records all actions taken by SmartPeak during a user's session. +The log is written to the user's hard drive :ref:`logs` and can also be viewed within the SmartPeak GUI ``view | logs``. +Each action or line-item in the log is groups according to message type (e.g., INFO, DEBUG, WARNING, ERROR, etc.). + +**Feature log** +The feature log records all features that were found in a sample along with all changes that were made to each feature during a user's session. +Each feature change is `time-stamped` so that there is complete provenance of any reported data generated by SmartPeak. +In addition, the feature log enables workflow checkpointing whereby a previously saved feature log for a particular sample can be loaded in a later session so that the user does not need to re-run a previously ran workflow for a sample. +Feature logs are recorded during the STORE_FEATURES and can be loaded using the LOAD_FEATURES workflow steps. +The `used` features can be visualized within the SmartPeak GUI using the various views provided. +The pyOpenMS python module can be used for further post processing and analysis of features in python (see https://github.com/AutoFlowResearch/BFAIR for examples). + +Automated data processing workflows and workflow execution engine +----------------------------------------------------------------------------- + +Data procesing workflow presets +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +SmartPeak has been used and optimized for various analytical chemistry workflows. +An example set of optimized workflows have been given presets within SmartPeak for faster selection and execution. + +.. image:: ../images/workflow_presets.png + +Please see :ref:`tutorials` for in depth walkthroughs for using each of the preset workflows. +The workflow presets are also a good starting point for developing a custom workflow. +Workflow steps can be added or removed using the GUI. + +.. image:: ../images/workflow_add_step.png + +Modified workflows can be saved to a ``workflow.csv`` file and loaded into SmartPeak. + +.. image:: ../images/workflow_save.png + +Workflow execution engine +~~~~~~~~~~~~~~~~~~~~~~~~~ + +SmartPeak includes a workflow engine that optimizes the order of workflow step executions and the resources used to process samples in parallel. +Before any workflow is executed, SmartPeak determines which workflow steps can be executed in parallel and which need to be executed in serial by analyzing the workflow step dependencies. + +.. image:: ../images/workflow_optimized.png + +The user has the option to specify the number of resources (i.e., CPU threads) that can be allocated to executing a workflow. +By default, the maximum number of threads available to the user will be used. +Once the order of workflow step executions and resources used to process samples in parallel are optimized, SmartPeak estimates the time needed to complete the workflow. + +.. image:: ../images/workflow_estimate_0.png + +The time estimate is continuously updated as the workflow is executed to better reflect operating conditions. + +.. image:: ../images/workflow_estimate_1.png + +The actual workflow time is logged and also displayed in the GUI. + +.. image:: ../images/workflow_estimate_2.png + +While the number of CPU cores/threads determines the number of samples that can be ran in parallel, it is important to note that the system memory (i.e., RAM) provides an upper limit on the number of samples that can be run during a single workflow. +If you find that workflows are taking a long time, we recommend profiling the system memory to see if your computer is out of memory. +Please see the :ref:`faq` for tips on how to improve system memory utilization for workflows involved large numbers of samples and large data files (e.g., non-targeted metabolomics). + +Workflow steps +~~~~~~~~~~~~~~ + +All workflow steps are written in modern C++ so that workflows are as fast and safe as possible. +Many of workflow steps that involve complex algorithms are wrappers around classes or functions that have been deposited in the open-source mass spectrometry library `OpenMS `_ an externally validated by the open-source community or scientific reviewers if the works were published in a peer-reviewed journal. +SmartPeak integrates with the classes and functions natively so that workflows can be executed in memory without the need for expensive and time consuming disk IO. +SmartPeak also provides logging, exception handling, and other facilities that would be expected of a professional application to ensure robust and reliable execution of open-source algorithms. +A complete list of workflow steps and their description can be found in the :ref:`faq`. +The SmartPeak team closely collaborates with the open-source community including with the developers at OpenMS, so if you have a workflow step request, please contact us. + +Creating, saving, and loading sessions +----------------------------------------------------------------------------- + +Usage +~~~~~ + +A custom database is used by SmartPeak to store all SmartPeak application data, which is called the "session object". +The data includes user input, algorithm parameters, workflow steps, workflow step outputs, and UI settings. +Certain user input and workflow step outputs are large (e.g., raw data files and feature files); SmartPeak does not store those directly, but stores the links to the files. +This enables a user to share a relatively small session object with colleagues so that they can visualize the results of a SmartPeak workflow and interact with the SmartPeak UI just as the user had done when they saved the session. +This also enables the user to re-run a workflow or further process a saved session from another computer so long as the computer has access to the files. +Note that the user will be prompted to update the session file links if SmartPeak detects that the links are no longer valid prior to running any workflow that requires access to the session file data. + +Example +~~~~~~~ + +After starting SmartPeak, create a new session by navigatin to ``file | new session``. + +.. image:: ../images/new_load_session.png + +A dialogue box to select the folder to load/save session files will be displayed. + +.. image:: ../images/create_session.png + +Files that have been named using the SmartPeak convention will be identified automatically. +The user can select alternative files as needed. +The modal will alert the user if missing sessions files are identified. + +.. image:: ../images/session_files.png + +The user can specify which files should be stored within the SmartPeak session object, and which remain external to the session object. + +.. image:: ../images/session_external_internal.png + +The user can save all application settings including the current UI view to the session object. + +.. image:: ../images/save_session.png + +Optimize calibration curves and quantitation methods +----------------------------------------------------------------------------- + +Usage +~~~~~ + +SmartPeak provides algorithms and workflow steps for automatically optimizing calibration curves. +The user must first specify the quantitation method for each component to use for each transition and the amount of standards for each component in the Standards samples. +The QuantitationMethods.csv and StandardsConcentrations.csv files, respectively, are used for these purposes. +The user can optimize all calibration curves automatically using the workflow steps for ``OPTIMIZE_CALIBRATION`` and ``STORE_QUANTITATION_METHODS``. +The user can then review all calibration curves in the GUI to further optimize the quantitation methods semi-manually. + +Example +~~~~~~~ + +After running the workflow, the calibration curves for each quantitation method are available to view. +The quantitation method parameters are shown on the left and the calibration curve and points are shown on the right. +The user has the option to view different components and sequence segments using the menu on the top left. +The user can also modify the quantitation method input parameters on the left. + +.. image:: ../images/calibrators.png + +Each point (i.e.., Injection) can be hovered over and a tooltip will display with additional information about that particular point + +.. image:: ../images/calibrators_tooltip.png + +Each point can be right clicked to bring up a menu that allows for showing the chromatogram for the point or including/excluding the point from the calibration curve. + +.. image:: ../images/calibrators_chromatogram_select.png + +Selecting ``Show chromatogram`` brings up the chromatogram view for that point. + +.. image:: ../images/calibrators_chromatogram.png + +Selecting ``Exclude from calibration`` will remove the point from the calibration curve. +If ``Fit calibration`` is selected in the ``Actions`` menu of the Calibrators view, the quantitation method will be re-calculated without the point included. +If ``Optimize calibrations`` is selected in the ``Actions`` menu of the Calibrators view, the quantitation method will be re-optimized using the workflow step ``OPTIMIZE_CALIBRATION``. + +.. image:: ../images/calibrators_refit.png + +A tabular view of all quantitation methods can be found under ``View | Workflow parameters | Quantitation methods``. + +.. image:: ../images/calibrators_quant_methods.png + +Select features from the "best" dilution ----------------------------------------------------------------------------- Usage ~~~~~ -Once workflow has been run, we sometimes know that we will have more interresting features to analyse compared to others depending on the dilution factor of the corresponding sample that produced this feature for a specific component. +Due to the orders of magnitude difference between different metabolite, lipid, and protein species concentrations in biological samples, one often needs to run the same sample at different concentrations to capture all of the different species within the limits of detection for the instrument. +After processing each of the different sample dilutions (referred to as dilution_factor in SmartPeak), the user often would like to select a specific dilution that a particular component should be reported because that dilution has been found to provide the best signal to noise ratio for that component. SmartPeak allows to specify this selection as a step of the ``MERGE_INJECTIONS`` workflow step using the ``select_preferred_dilution`` parameter (false by default). @@ -27,7 +189,7 @@ When ``select_preferred_dilution`` is set to true, SmartPeak will look for a fil * - arg-L.arg-L_1.Light - 1 -During the ``MERGE_INJECTIONS`` all components from the features that are listed the file and to which the injection dilution does not correspond to the value set in the select_preferred_dilutions_file will be removed. The ``MERGE_INJECTIONS`` will be then applied as usual. +During the ``MERGE_INJECTIONS`` all components from the features that are listed in the file and to which the injection dilution does not correspond to the value set in the select_preferred_dilutions_file will be removed. The ``MERGE_INJECTIONS`` will be then applied as usual. Example ~~~~~~~ @@ -123,3 +285,48 @@ Indeed the feature database willl show us that it is the maximum ``peak_apex_int .. image:: ../images/select_dilutions_featuresdb.png Now, in our dilution file, if we set trp-L.trp-L_1.Heavy to preferred dilution_factor 1, the result will be 137, which is the maximum ``peak_apex_int`` from the sample based on dilution 1. + +Optimize workflow step algorithm parameters +----------------------------------------------------------------------------- + +Usage +~~~~~ + +.. todo:: + Describe the usage. + +Example +~~~~~~~ + +.. todo:: + Provide an example. + +Debug feature picking, selection, and filtering (and acquisition methods) +----------------------------------------------------------------------------- + +Usage +~~~~~ + +.. todo:: + Describe the usage. + +Example +~~~~~~~ + +.. todo:: + Provide an example. + +Enable automated QC/QA of workflows +----------------------------------------------------------------------------- + +Usage +~~~~~ + +.. todo:: + Describe the usage. + +Example +~~~~~~~ + +.. todo:: + Provide an example. \ No newline at end of file diff --git a/docs/start/start.rst b/docs/start/start.rst index 46e9e3baf..6efff5242 100644 --- a/docs/start/start.rst +++ b/docs/start/start.rst @@ -5,6 +5,7 @@ Getting started with SmartPeak :start-after: begin_introduction :end-before: end_introduction +.. image:: ../images/Fig01_SmartPeak_overview.jpg Quick Start ----------- @@ -13,8 +14,10 @@ Download SmartPeak from `GitHub - 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