diff --git a/conf.py b/conf.py index eddbdf24..9fe98ca3 100644 --- a/conf.py +++ b/conf.py @@ -37,6 +37,7 @@ 'myst_parser', 'notfound.extension', 'sphinxcontrib.images', + 'sphinx_inline_tabs', ] autosummary_generate = True diff --git a/docs/additional-resources/openms-git-workflow.md b/docs/additional-resources/openms-git-workflow.md index dfa2ee22..0272eb98 100644 --- a/docs/additional-resources/openms-git-workflow.md +++ b/docs/additional-resources/openms-git-workflow.md @@ -14,8 +14,8 @@ Naming conventions for the following apply: * A **local repository** is the repository that lies on your hard drive after cloning. * A **remote repository** is a repository on a git server such as GitHub. * A **fork** is a copy of a repository. Forking a repository allows you to freely experiment with changes without affecting the original project. -* **Origin** refers to a remote repository that you have forked. Call this repository https://github.com/_YOURUSERNAME_/OpenMS. -* **Upstream** refers to the original remote OpenMS repository. Call this repository https://github.com/OpenMS/OpenMS. +* **Origin** refers to a remote repository that you have forked. Call this repository `https://github.com/_YOURUSERNAME_/OpenMS`. +* **Upstream** refers to the original remote OpenMS repository. Call this repository `https://github.com/OpenMS/OpenMS`. ## Create fork diff --git a/docs/contact-us.md b/docs/contact-us.md index b46e0625..3f450fd3 100644 --- a/docs/contact-us.md +++ b/docs/contact-us.md @@ -1,9 +1,11 @@ Contact Us ========= -Contact us: +Join us on [Discord](https://discord.com/invite/swkxs72CHB)! -1. Using the user and contributor real time [Gitter chat](https://gitter.im/OpenMS/OpenMS). +You can also contact us: + +1. On the user and contributor real time [Gitter chat](https://gitter.im/OpenMS/OpenMS). 2. Drop us an email at user support [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) mailing list. 3. To stay updated of new versions of OpenMS and releases, subscribe to [openms-announcements mailing list](https://sourceforge.net/projects/open-ms/lists/open-ms-announcements). diff --git a/docs/downloads.md b/docs/downloads.md index 2f1d586e..94fec0a2 100644 --- a/docs/downloads.md +++ b/docs/downloads.md @@ -1,9 +1,4 @@ -Downloads -======== - -Download OpenMS installers, workflows, and other resources. - -# OpenMS installers +# OpenMS Installers | Platform | Name | SHA256 Hash | |----------|------|-------------| @@ -17,27 +12,27 @@ Download OpenMS installers, workflows, and other resources. | Workflow | Description | Download Link | |----------|-------------|---------------| -|ProteomicsLFQ_tool_and_MSstats_postprocessing | Label-free identification and quantification using the comet search engine, the ProteomicsLFQ tool and statistical down-stream processing using MSstats. Compared to the other proteomics LFQ workflows, it is less complex as it combines quantification and inference steps in a single ProtemicLFQ tool. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/ProteomicsLFQ_tool_and_MSstats_postprocessing.knwf?raw=true) | -| basic_peptide_identification | Label-free identification using the omssa search engine. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/basic_peptide_identification.knwf?raw=true) | -| DIAMetAlyzer | Metabolomics assay library construction with decoy generation from DDA data and targeted DIA analysis using OpenSWATH and pyprophet for statistical validation. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/DIAMetAlyzer.knwf?raw=true) | -| Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT | Identification and quantification for isobaric experiments using MSGFPlus as search engine, epifany for inference and MSstatsTMT for statistical down-stream analysis. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT.knwf?raw=true) | -| labelfree_with_protein_quantification | Label-free with protein quantification steps implemented using individual OpenMS tools | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/labelfree_with_protein_quantification.knwf?raw=true) | -| Metabolite_Adduct_Grouping | Quantification and identification via accurate mass based on multiple adduct grouping steps (adducts, neutral losses). | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_Adduct_Grouping.knwf?raw=true) | -| Metabolite_DeNovoID | Quantification and identification via adduct grouping and de-novo identification using SIRIUS/CSI:FingerID. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_DeNovoID.knwf?raw=true) | -| Metabolite_ID | Quantification and identification via accurate mass based with downstream processing and visualisation. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_ID.knwf?raw=true) | -| Metabolite_SpectralID | Identification via spectral library search for small molecules. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_SpectralID.knwf?raw=true) | -| MSstats_statPostProcessing_iPRG2015 | Post processing workflow for using MSstats based on "Example_OneTool_ProteomicsLFQ_MSstats.knwf" | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/MSstats_statPostProcessing_iPRG2015.knwf?raw=true) | -| MSstatsTMT | Post processing workflow for using MSstatsTMT based on "Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT". | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/MSstatsTMT.knwf?raw=true) | -| OpenSWATH | Targeted extraction and scoring of transitions in DIA data based on an (iRT) assay library. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/OpenSWATH.knwf?raw=true) | -| Phosphoproteomics_ID | Identification of Phosphorilation sites. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Phosphoproteomics_ID.knwf?raw=true) | +|`ProteomicsLFQ_tool_and_MSstats_postprocessing` | Label-free identification and quantification using the comet search engine, the ProteomicsLFQ tool and statistical down-stream processing using MSstats. Compared to the other proteomics LFQ workflows, it is less complex as it combines quantification and inference steps in a single ProtemicLFQ tool. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/ProteomicsLFQ_tool_and_MSstats_postprocessing.knwf?raw=true) | +|`basic_peptide_identification` | Label-free identification using the omssa search engine. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/basic_peptide_identification.knwf?raw=true) | +|`DIAMetAlyzer` | Metabolomics assay library construction with decoy generation from DDA data and targeted DIA analysis using OpenSWATH and pyprophet for statistical validation. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/DIAMetAlyzer.knwf?raw=true) | +|`Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT` | Identification and quantification for isobaric experiments using MSGFPlus as search engine, epifany for inference and MSstatsTMT for statistical down-stream analysis. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT.knwf?raw=true) | +|`labelfree_with_protein_quantification` | Label-free with protein quantification steps implemented using individual OpenMS tools | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/labelfree_with_protein_quantification.knwf?raw=true) | +|`Metabolite_Adduct_Grouping` | Quantification and identification via accurate mass based on multiple adduct grouping steps (adducts, neutral losses). | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_Adduct_Grouping.knwf?raw=true) | +|`Metabolite_DeNovoID` | Quantification and identification via adduct grouping and de-novo identification using SIRIUS/CSI:FingerID. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_DeNovoID.knwf?raw=true) | +|`Metabolite_ID` | Quantification and identification via accurate mass based with downstream processing and visualisation. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_ID.knwf?raw=true) | +|`Metabolite_SpectralID` | Identification via spectral library search for small molecules. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_SpectralID.knwf?raw=true) | +|`MSstats_statPostProcessing_iPRG2015` | Post processing workflow for using MSstats based on "Example_OneTool_ProteomicsLFQ_MSstats.knwf" | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/MSstats_statPostProcessing_iPRG2015.knwf?raw=true) | +|`MSstatsTMT` | Post processing workflow for using MSstatsTMT based on "Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT". | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/MSstatsTMT.knwf?raw=true) | +|`OpenSWATH` | Targeted extraction and scoring of transitions in DIA data based on an (iRT) assay library. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/OpenSWATH.knwf?raw=true) | +|`Phosphoproteomics_ID` | Identification of Phosphorilation sites. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Phosphoproteomics_ID.knwf?raw=true) | # OpenMS Releases -| Release | Installers | -|---------|-------------| -| Stable release | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/) | -| RC release | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/RC/) | -| Nightly release | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/) | +| Release | Installers | +|--------------------------------------------------------|-------------| +| Stable release | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/) | +| RC release | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/RC/) | +| Nightly release | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/) | # Other Resources diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md index 4ca93ea3..6e7fadf6 100644 --- a/docs/guides/user-guides/user-quickstart-guide.md +++ b/docs/guides/user-guides/user-quickstart-guide.md @@ -2,14 +2,14 @@ User Quickstart Guide ==================== Read the User Quickstart guide to gain a brief understanding of key concepts and how to use the tools. For more in-depth -information, consult [OpenMS documentation](). +information, consult [OpenMS API Reference](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/index.html). ## What is OpenMS -[OpenMS.org](https://www.openms.de/) is a free, open-source C++ library with Python bindings. It is commonly used for liquid +[OpenMS](https://www.openms.de/) is a free, open-source C++ library with Python bindings. It is commonly used for liquid chromatography-mass spectrometry (LC-MS) data management and analyses. OpenMS provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it. OpenMS is available -under the three clause BSD licence and runs under Windows, macOS, and Linux operating systems. +under the [three clause BSD licence](https://github.com/OpenMS/OpenMS/blob/develop/LICENSE) and runs under Windows, macOS, and Linux operating systems. ## Background diff --git a/docs/index.rst b/docs/index.rst index aab0b3ef..3b5398b0 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -42,6 +42,7 @@ Contents installations/installation-on-gnu-linux installations/installation-on-windows installations/installation-on-macos + installations/build-openms-from-source .. toctree:: :maxdepth: 2 diff --git a/docs/installations/installation-on-macos.md b/docs/installations/installation-on-macos.md index 7e879ab9..a40ec8df 100644 --- a/docs/installations/installation-on-macos.md +++ b/docs/installations/installation-on-macos.md @@ -8,25 +8,25 @@ To install OpenMS on macOS, run the following steps: 1. Download and install the macOS drag-and-drop installer from the [archive](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/). 2. Double click on the dowloaded file. It will start to open the download `openms--macos.dmg` file -Verifying OpenMS-<version>-macOS.dmg +Verifying OpenMS-<version>-macOS.dmg 3. Verify the download. -Verifying OpenMS-<version>-macOS.dmg +Verifying OpenMS-<version>-macOS.dmg 4. Agree the license agreements. -License Agreement +License Agreement 5. Drag openms to applications. -License Agreement +License Agreement 6. It will start copying to applications. -Preparing to Copy to Applications +Preparing to Copy to Applications -Copying to Applications +Copying to Applications To use TOPP as regular app in the shell, add the following lines to the `~/.profile` file. diff --git a/docs/introduction.md b/docs/introduction.md index d22c856c..015811f2 100644 --- a/docs/introduction.md +++ b/docs/introduction.md @@ -26,7 +26,7 @@ of ions are stored in mass spectra and used to identify and quantify the analyte methods. The quantity and identity of analytes can then be used, for instance, in biomarker discovery, medical diagnostics, or basic research. -# Liquid Chromatography(LC) +## Liquid Chromatography(LC) LC aims to reduce the complexity of the measured sample by separating analytes based on their physicochemical properties. Separating analytes in time ensures that a manageable amount of analytes elute at the same time. In mass @@ -45,7 +45,7 @@ spectrometer. ![](images/introduction/introduction_LC.png) -# Mass Spectrometry +## Mass Spectrometry MS is an analytical technique used to determine the mass of molecules. In order to achieve highly accurate and sensitive mass measurements at the atomic scale, mass spectrometers manipulate charged particles using magnetic and electrostatic @@ -87,3 +87,19 @@ spectrometry (MS/MS) can be applied to assess the analyte substructure. To this kinetically fragmented using an inert gas (e.g., Argon). Fragments produced by collision-induced fragmentation (CID) are stored in an MS2 (or MS/MS) spectrum and provide information that helps to resolve the ambiguities in identification. Alternatively, MS/MS spectra can be used for quantification. + +Get started with installing OpenMS using the installers available for different operating systems! + +## Installation on different platforms + +```{tab} GNU/Linux +wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Debian-Linux-x86_64.deb +``` + +```{tab} Windows +wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Win64.exe +``` + +```{tab} MacOS +wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-macOS.dmg +``` diff --git a/docs/topp/topp.md b/docs/topp/topp.md index adead82c..edfb7fe8 100644 --- a/docs/topp/topp.md +++ b/docs/topp/topp.md @@ -10,7 +10,13 @@ experiments and OpenSWATH, peptide property prediction, cross-linking, quality-c Few of the graphical tools are explained below: -- [TOPPView](toppview.md): A viewer for mass spectrometry data. -- [TOPPAS](toppas.md): An assistant for GUI-driven TOPP workflow design. -- [INIFileEditor](ini-file-editor.md): An editor for OpenMS configuration files. -- [SwathWizard](swathwizard.md): A user-friendly step-by-step wizard for SWATH data analysis. +```{toctree} +:maxdepth: 1 + +toppview: A viewer for mass spectrometry data. +toppas: An assistant for GUI-driven TOPP workflow design. +ini-file-editor: An editor for OpenMS configuration files. +swathwizard: A user-friendly step-by-step wizard for SWATH data analysis. +``` + +For advanced documentation on every TOPP tool, see the [OpenMS TOPP API Reference](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html). diff --git a/docs/tutorials/TOPP/TOPP-tutorial.md b/docs/tutorials/TOPP/TOPP-tutorial.md index cdbc3502..76e29b3f 100644 --- a/docs/tutorials/TOPP/TOPP-tutorial.md +++ b/docs/tutorials/TOPP/TOPP-tutorial.md @@ -6,48 +6,72 @@ compared to OpenMS. Later, we will move to the handling of TOPPView which is our TOPPView can also be used to analyze it using selected TOPP tools; how-to is explained in the third part of the tutorial. Finally, the tutorial lists the command line interfaces for all TOPP tools contained in the release. -## Concepts +# Concepts Let's understand the intent of [TOPP and OpenMS](topp-and-openms-introduction.md) in this part. -## TOPPView Main Interface +```{toctree} +:maxdepth: 1 + +topp-and-openms-introduction +``` + +# TOPPView Main Interface In this part of the tutorial, we will learn about the main features of TOPPView and its basic uses. -- [TOPPView introduction](toppview-introduction.md) -- [Views in TOPPView](views-in-toppview.md) -- [Display modes and view options](display-modes-and-view-options.md) -- [Data analysis in TOPPView](data-analysis-in-toppview.md) -- [Data editing](data-editing-in-toppview.md) -- [Hotkeys](hotkeys-table.md) +```{toctree} +:maxdepth: 1 -## Calling TOPP tools from TOPPView +toppview-introduction +views-in-toppview +display-modes-and-view-options +data-analysis-in-toppview +data-editing-in-toppview +hotkeys-table +``` + +# Calling TOPP tools from TOPPView This part of the tutorial illustrates how to interactively analyse proteomics data using TOPP tools from within TOPPView. -- [Smoothing raw data](smoothing-raw-data.md) -- [Subtracting a baseline from a spectrum](subtracting-a-baseline-from-a-spectrum.md) -- [Picking peaks](picking-peaks.md) -- [Feature detection on centroided data](feature-detection-on-centroided-data.md) +```{toctree} +:maxdepth: 1 + +smoothing-raw-data +subtracting-a-baseline-from-a-spectrum +picking-peaks +feature-detection-on-centroided-data +``` -## Advanced Users: Tips & Tricks +# Advanced Users: Tips & Tricks Read [TOPP for Advanced Users](topp-for-advanced-users.md) to know more about how to use advanced functionalities, increasing productivity. -## Scripting with TOPP +```{toctree} +:maxdepth: 1 + +topp-for-advanced-users +``` + +# Scripting with TOPP This part of the tutorial gives a detailed overview of the most important TOPP tools. First, some basics needed for every TOPP tool are explained, then several example pipelines are shown. -- [General introduction](general-introduction.md) -- [File Handling](file-handling.md) -- [Profile data processing](profile-data-processing.md) -- [Calibration](calibration.md) -- [Map alignment](map-alignment.md) -- [Feature detection](feature-detection.md) -- [Feature grouping](feature-grouping.md) -- [Consensus peptide identification](consensus-peptide-identification.md) -- [Peptide property prediction](peptide-property-prediction.md) -- [Quality control](quality-control.md) -- [Conversion between OpenMS XML formats and text formats](conversion-between-openms-xml-formats-and-text-formats.md) +```{toctree} +:maxdepth: 1 + +general-introduction +file-handling +profile-data-processing +calibration +map-alignment +feature-detection +feature-grouping +consensus-peptide-identification +peptide-property-prediction +quality-control +conversion-between-openms-xml-formats-and-text-formats +``` diff --git a/docs/tutorials/TOPP/calibration.md b/docs/tutorials/TOPP/calibration.md index c570e6cc..fa65e17b 100644 --- a/docs/tutorials/TOPP/calibration.md +++ b/docs/tutorials/TOPP/calibration.md @@ -3,7 +3,7 @@ Calibration OpenMS offer two calibration methods: an internal and an external calibration. Both can handle peak data as well as profile data. To calibrate profile data, a peak picking step is necessary, the important parameters can be set via the -ini-file. If you have already picked data, don't forget the `-peak\_data` flag. +ini-file. If you have already picked data, don't forget the `-peak_data` flag. The external calibration (**TOFCalibration**) is used to convert flight times into m/z values with the help of external calibrant spectra containing e.g. a polymer like polylysine. For the calibrant spectra, the calibration constants the diff --git a/docs/tutorials/TOPP/hotkeys-table.md b/docs/tutorials/TOPP/hotkeys-table.md index 9d4ef4a7..600e7f51 100644 --- a/docs/tutorials/TOPP/hotkeys-table.md +++ b/docs/tutorials/TOPP/hotkeys-table.md @@ -3,18 +3,18 @@ TOPPView Hotkeys ## File handling -| Hotkey | Function | -|----------------------|-----------------------------------------------------| -| CTRL + O | Open file | -| CTRL + W | Close current window | -| CTRL + S | Save current layer | +| Hotkey | Function | +|---------------------------------------------------------|-----------------------------------------------------| +| CTRL + O | Open file | +| CTRL + W | Close current window | +| CTRL + S | Save current layer | | CTRL + SHIFT + S | Save visible data of current layer | ## Navigation in the data | Hotkey | Function | -|----------------------|-----------------------------------------------------| +|------------------------------------|-----------------------------------------------------| | CTRL | Activate zoom mode | | SHIFT | Activate measurement mode | | Arrow keys | Translate currently shown data (1D View: Shift + Left/Right moves to the next peak in sparse data)| @@ -25,6 +25,7 @@ TOPPView Hotkeys | PageUp | Select previous layer | | PageDown | Select next layer | + ## Visualization options | Hotkey | Function | @@ -47,31 +48,31 @@ kbd>Home on macOS keyboards is also Fn + ArrowLeft. ## Annotations in 1D view -| Hotkey | Function | -|----------------------|-----------------------------------------------------| +| Hotkey | Function | +|------------------------------------------|-----------------------------------------------------| | CTRL + A | Select all annotations of the current layer | -| DEL | Delete all currently selected annotations | +| DEL | Delete all currently selected annotations | + ## Advanced -| Hotkey | Function | -|----------------------|-----------------------------------------------------| -| CTRL + T | Apply TOPP tool to the current layer | +| Hotkey | Function | +|-----------------------------------------------------|---------------------------------------------------------| +| CTRL + T | Apply TOPP tool to the current layer | | CTRL + SHIFT + T | Apply TOPP tool to the visible data of the current layer| -| F4 | Re-run TOPP tool | -| CTRL + M | Show layer meta information | -| CTRL + I | Annotate with identification results | -| 1 | Show precursor peaks (2D peak layer) | -| 2 | Show projections (2D peak layer) | -| 5 | Show overall convex hull (2D feature layer) | -| 6 | Show all convex hulls (2D feature layer) | -| 7 | Show numbers and labels (2D feature layer) | -| 9 | Show consensus elements (2D consensus layer) | +| F4 | Re-run TOPP tool | +| CTRL + M | Show layer meta information | +| CTRL + I | Annotate with identification results | +| 1 | Show precursor peaks (2D peak layer) | +| 2 | Show projections (2D peak layer) | +| 5 | Show overall convex hull (2D feature layer) | +| 6 | Show all convex hulls (2D feature layer) | +| 7 | Show numbers and labels (2D feature layer) | +| 9 | Show consensus elements (2D consensus layer) | ## Help - -| Hotkey | Function | -|----------------------|-----------------------------------------------------| -| F1 | Show TOPPView online tutorial | +| Hotkey | Function | +|----------------------------------------|-----------------------------------------------------| +| F1 | Show TOPPView online tutorial | | SHIFT + F1 | Activate *What's this?* mode | diff --git a/docs/tutorials/TOPP/picking-peaks.md b/docs/tutorials/TOPP/picking-peaks.md index 2b397e47..b31845b4 100644 --- a/docs/tutorials/TOPP/picking-peaks.md +++ b/docs/tutorials/TOPP/picking-peaks.md @@ -9,7 +9,7 @@ There are two types of PeakPickers: the **PeakPickerWavelet** and one especially examples data (select **File** > **Open example data**). The main parameters are the peak width and the minimal signal to noise ratio for a peak to be picked. If you don't know -the approximate `fwhm` of peaks, use the estimation included in the PeakPickerWavelet, set the flag `estimate\_peak\_width` +the approximate `fwhm` of peaks, use the estimation included in the PeakPickerWavelet, set the flag `estimate_peak_width` to `true`. After applying the PeakPickerWavelet, observe which peak width was estimated and used for peak picking in the log window. @@ -18,7 +18,7 @@ the fwhm of one or several representative peaks. If the peak picker delivers only a few peaks even though the `peak_with` and `signal_to_noise` parameters are set to good values, consider changing the advanced parameter `fwhm_lower_bound_factor` to a lower value. All peaks with a lower -`fwhm` than `fwhm_lower_bound_factor` \* `peak\_width` are discarded. +`fwhm` than `fwhm_lower_bound_factor` \* `peak_width` are discarded. The following image shows a part of the spectrum with the picked peaks shown in green, the estimated peak width in the log window and the measured peak width. diff --git a/docs/tutorials/TOPP/quality-control.md b/docs/tutorials/TOPP/quality-control.md index 1ffd78b7..6f7060fd 100644 --- a/docs/tutorials/TOPP/quality-control.md +++ b/docs/tutorials/TOPP/quality-control.md @@ -1,12 +1,12 @@ Quality Control =============== -To check the quality of the data (supports label-free workflows and [TOPP Documentation:IsobaricAnalyzer](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html) output): +To check the quality of the data (supports label-free workflows and [IsobaricAnalyzer](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html) output): -The [TOPP Documentation:QualityControl](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_QualityControl.html) TOPP tool computes and collects data which allows to compute QC metrics to check the quality of +The [QualityControl](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_QualityControl.html) TOPP tool computes and collects data which allows to compute QC metrics to check the quality of LC-MS data. Depending on the given input data, this tool collects data for metrics (see section [Metrics](quality-control.md#Metrics)). New metavalues will be added to existing data and the information will be written out in mzTab format. This mzTab file can -then be processed using custom scripts or via the R package (see [github:cbielow:PTXQC](https://github.com/cbielow/PTXQC/). +then be processed using custom scripts or via the R package (see [PTXQC](https://github.com/cbielow/PTXQC/). ## Workflow @@ -14,8 +14,8 @@ then be processed using custom scripts or via the R package (see [github:cbielow Find an example workflow in `OpenMS/share/OpenMS/examples/TOPPAS/QualityControl.toppas`. -For data from [TOPP Documentation:IsobaricAnalyzer](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html), just provide the consensusXML as input to -[TOPP Documentation:QualityControl](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_QualityControl.html). No FeatureXMLs or TrafoXMLs are required. The mzML raw file can be added as input though. +For data from [IsobaricAnalyzer](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html), just provide the consensusXML as input to +[QualityControl](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_QualityControl.html). No FeatureXMLs or TrafoXMLs are required. The mzML raw file can be added as input though. ## Metrics @@ -122,10 +122,10 @@ PostFDR FeatureXML, raw mzML file. ### MzCalibration -The **MzCalibration** metric adds new metavalues to the first (best) hit of each PeptideIdentification. For this metric it is also possible -to use this without an MzML File, but then only uncalibrated m/z error (ppm) will be reported. However for full -functionality a PeakMap/MSExperiment with original m/z-values before m/z calibration generated by InternalCalibration -has to be given. +The **MzCalibration** metric adds new metavalues to the first (best) hit of each PeptideIdentification. For this metric +it is also possible to use this without an MzML File, but then only uncalibrated m/z error (ppm) will be reported. +However, for full functionality a PeakMap/MSExperiment with original m/z-values before m/z calibration generated by +InternalCalibration has to be given. #### Required input data @@ -145,8 +145,8 @@ PostFDR FeatureXML ### RTAlignment -The **RTAlignment** metric checks what the retention time was before the alignment and how it is after the alignment. These -two values are added to the metavalues in the PeptideIdentification. +The **RTAlignment** metric checks what the retention time was before the alignment and how it is after the alignment. +These two values are added to the metavalues in the PeptideIdentification. #### Required input data diff --git a/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md b/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md index ff7227ef..f0f9e7c1 100644 --- a/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md +++ b/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md @@ -2,7 +2,7 @@ Subtracting a Baseline from a Spectrum ===================================== First, load the spectrum to be analyzed in TOPPView. To use the described tools, open the tutorial data via the -File-menu (**File** > **Open example file**, then select `peakpicker\_tutorial\_1.mzML`). The BaselineFilter can be called via +File-menu (**File** > **Open example file**, then select `peakpicker_tutorial_1.mzML`). The BaselineFilter can be called via the Tools-menu (**Tools** > **Apply TOPP tool**), then select **BaselineFilter** as TOPPtool (red rectangle). You can choose, between different types of filters (green rectangle), the one mainly used is TopHat. The other important parameter is the length of the structuring element (blue rectangle). The default value is `3` Thomson. Press **Ok** to start the baseline diff --git a/docs/tutorials/TOPP/topp-for-advanced-users.md b/docs/tutorials/TOPP/topp-for-advanced-users.md index 5f327f9a..306df58c 100644 --- a/docs/tutorials/TOPP/topp-for-advanced-users.md +++ b/docs/tutorials/TOPP/topp-for-advanced-users.md @@ -6,7 +6,7 @@ This tutorials has some advanced concepts of TOPP, which will increase productiv ## Global database for search engine adapters In your `$HOME` directory find an `OpenMS.ini` in the `.OpenMS` subfolder. This INI file contains global parameters -which are used by many/all TOPP tools, depending on what the parameters refer to. The `id\_db\_dir` parameter allows to +which are used by many/all TOPP tools, depending on what the parameters refer to. The `id_db_dir` parameter allows to specify one or more directories where FASTA files (or related, e.g., `.psq` files) are placed. Specified filename (without path) in an ID engine adapter, will be looked up in the current working directory. If its not found, the directories specified in `id_db_dir` will be searched. This allows to build scripts and/or TOPPAS pipelines which are @@ -30,6 +30,6 @@ INI settings portable. OpenMS supports the wrapping of external tools (like msconvert from ProteoWizard), thus allowing to build scripts and/or TOPPAS pipelines containing external tools. -**See also** - - `share/OpenMS/TOOLS/EXTERNAL/ReadMe.txt` in your local installation for details. +```{seealso} +`share/OpenMS/TOOLS/EXTERNAL/ReadMe.txt` in your local installation for details. +``` diff --git a/docs/tutorials/TOPPAS/TOPPAS-tutorial.md b/docs/tutorials/TOPPAS/TOPPAS-tutorial.md index 98e06e29..10e721d4 100644 --- a/docs/tutorials/TOPPAS/TOPPAS-tutorial.md +++ b/docs/tutorials/TOPPAS/TOPPAS-tutorial.md @@ -5,6 +5,10 @@ TOPPAS Tutorial The parameters of all involved tools can be edited within TOPPAS and are also saved as part of the pipeline definition in the `.toppas` file. - - [General introduction](general-introduction.md) - - [User interface](user-interface.md) - - [Examples](examples.md) +```{toctree} +:maxdepth: 1 + + general-introduction + user-interface + examples + ``` diff --git a/requirements.txt b/requirements.txt index 862245ba..06400885 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,4 +5,5 @@ sphinx-copybutton myst-parser sphinx-notfound-page sphinxcontrib-images +sphinx-inline-tabs pygments