data support update

docs/data_conversion.md

@@ -1,27 +1,66 @@
 # Data handling (supported formats)
 
-mzmine supports both **open** (e.g., .mzML, .mzXML, .imzML, .netCDF) and **proprietary**
-formats from Bruker Daltonics (.d and .tdf/tsf). Raw data files from 
-vendors must be converted into an open format prior to the import. **This conversion can be applied automatically
-during the import, if the user has MSConvert installed.** 
-If you want to convert the files yourself, see the sections below.
-
-The **recommendations** for the data handling are the conversion of the raw data to centroided .mzML
-data files,
-**except** for timsTOF data (native .tdf and .tsf inside the Bruker .d folder), and the conversion of MS
-imaging data to .imzML, except for the timsTOF fleX MS imaging data.
+mzmine supports both **open** (e.g., .mzML, .mzXML, .imzML, .netCDF) and many **proprietary** 
+vendor data formats. For many vendor formats it is recommended to use the original data files and 
+to only apply conversion where needed. Data files can be imported by drag-and-dropping files into 
+the mzmine graphical user interface or using the _import MS data_ module. 
+
+**Supported raw data formats include:**
+- Bruker Daltonics (.d and .tdf/tsf) 
+- Thermo Fisher (.raw)
+- Waters (.raw folders)
+- Agilent (.d)
+- Sciex (.wiff/.wiff2)
+- Shimadzu (.lcd)
+- MOBILion (.mbi)
+- mzML or mzXML/mzData/netCDF (prefer mzML if possible due to better metadata coverage)
+- imzML (MS imaging)
+
+!!! warning
+
+    Some vendor data formats are only supported on specific operating systems due to the limited 
+    support by their respective data access libraries. All data formats are supported on Windows 
+    and many on Linux (see full [compatibility list here](system_requirements.md#compatibility)).
+    Many data formats are unsupported on macOS, requiring data conversion to open formats, usually
+    on a Windows or Linux computer.
+
+## External dependencies
+
+Many data formats are supported without external dependencies, directly through the mzmine version.
+Other formats may require another third-party software to be downloaded and installed.
+
+**MSConvert:** This tool is provided by ProteoWizard and the default data converter for MS data. 
+While our team is expanding the native data support for all major vendor formats, we recommend to
+install MSConvert for some formats. This will grant direct access to these files and mzmine will
+use MSConvert with some internal optimizations to load data files in the background. Formats that 
+currently require MSConvert for direct support include:
+- Agilent (.d)
+- Sciex (.wiff/.wiff2)
+- Shimadzu (.lcd)
+- MOBILion (.mbi)
 
 ## Data conversion to open formats (.mzML / .imzML)
 
+When converting data, prefer the latest standard formats mzML (or imzML for MS imaging data).
+Other older open formats like mzData or mzXML may cover less metadata.
+It is **recommended** to convert raw data to centroided .mzML files.
+**Exceptions:** timsTOF native data as .tdf and .tsf inside the Bruker .d folder are best imported 
+in their original format. This is also true for timsTOF fleX MS imaging data.
+
+**This conversion can be applied automatically during the import if the user has MSConvert installed.**
+If you want to convert the files yourself, see the sections below.
+
+
 ### MSConvert (ProteoWizard) to mzML
 
 !!! info
 
-    mzmine can use MSConvert automatically. Make sure to setup the MSConvert installation path in the mzmine preferences. (only supported on Windows)
+    mzmine can use MSConvert automatically. Make sure to setup the MSConvert installation path in 
+    the mzmine preferences. (only supported on Windows)
 
 ![MSConvert_settings](MSConvert_settings.png)
 
-MSConvert supports the conversion of AB SCIEX, Agilent, Bruker, Shimadzu, Thermo Scientific,
+MSConvert supports the conversion of AB SCIEX, Agilent, Bruker, Shimadzu, Thermo Scientific, MOBILion,
 and [Waters](data_conversion.md#waters) raw data. More information about the formats can be found in
 the [ProteoWizard Documentation for Users](https://proteowizard.sourceforge.io/doc_users.html).
 Furthermore, profile data can be centroided to reduce the file size and memory consumption,
@@ -62,17 +101,19 @@ the [ProteoWizard documentation](https://proteowizard.sourceforge.io/tools/mscon
 ### ThermoRawFileParser
 
 It is used to convert ThermoFisher .raw files into .mgf, .mzML, .parquet. This converter is
-important if an
-internal calibrant was used (e.g., EASY-IC). This mass is excluded in the FreeStyle view, whereas
-MSConvert
-remains all signals in the mzML, including the calibrant. If those masses together with some flagged signals
-by Thermo, should be
-removed use this converter with the option --excludeExceptionData.
+important if an internal calibrant was used (e.g., EASY-IC). This mass is excluded in the FreeStyle
+view, whereas MSConvert remains all signals in the mzML, including the calibrant. If those masses 
+together with some flagged signals by Thermo, should be removed use this converter with the option 
+**--excludeExceptionData**.
 
 !!! Note
 
-    mzmine can use the ThermoRawFileParser automatically to import your data without conversion. In the preferences (CTRL+P) 
-    set the "Thermo data import" to "Thermo raw file parser" instead of MSConvert. The raw file parser is supported on Mac, Linux, and Windows.
+    **mzmine 4.8** and higher supports Thermo Raw data directly, there is no need to install external 
+    dependencies.
+
+    **Earlier mzmine versions** can use the ThermoRawFileParser automatically to import your data 
+    without conversion. In the preferences (CTRL+P) set the "Thermo data import" to "Thermo raw 
+    file parser" instead of MSConvert. The raw file parser is supported on Mac, Linux, and Windows.
 
 Example for command line interface with the exclusion of exception data:
 
@@ -105,6 +146,8 @@ how to use it can be found [here](https://github.com/elnurgar/mzxml-precursor-co
 
 ### Waters
 
+Direct Waters data support is currently in beta phase. 
+
 Waters recently released a tool called **Waters data connect**, which allows conversion of DDA, DIA,
 and HD-DDA data to mzML. Lock mass correction is applied during the conversion. We also recommend to
 enable centroiding (2D peak picking).

docs/system_requirements.md

@@ -4,7 +4,7 @@
 
 Installation of mzmine is described on the [getting started](getting_started.md#install-update) page.
 mzmine is available as an installable package or a portable version. The portable version does not
-require administator rights to be run, making it useful for university students without elevated
+require administrator rights to be run, making it useful for users without elevated
 permissions.
 
 ## Hardware requirements
@@ -38,16 +38,12 @@ permissions.
 
 <!-- markdown-link-check-disable -->
 
-- Up-to-date operating system, e.g., Windows 10 or newer, recent Linux or MacOS (academic only) versions
-- mzmine does not require a dedicated Java installation, even though it is a Java software. All
-requirements are shipped with mzmine
+- Up-to-date operating system, e.g., Windows 10 or newer, recent Linux or MacOS (academic only) versions. 
+- mzmine does not require a dedicated Java installation, as it is a self-contained Java software with its own Java Virtual Machine. All
+requirements are shipped with mzmine.
 - Microsoft Visual Studio C++ Redist for Bruker raw data import [download page](https://learn.microsoft.com/de-de/cpp/windows/latest-supported-vc-redist?view=msvc-170)
-- MSConvert (on Windows) for native Sciex, Waters, Shimadzu, MOBILion, Thermo data
-  support [download page](https://proteowizard.sourceforge.io/download.html)
-    - Thermo alternative: ThermoRawFileParser for native Thermo support on Windows, Mac, and
-      Linux [download page](https://github.com/pluskal-lab/ThermoRawFileParserMacLinux/releases)
-    - ThermoRawFileParser does not need to be installed but only downloaded and imported via the
-      mzmine preferences
+- MSConvert (on Windows) for native Agilent, Sciex, Waters, Shimadzu, and MOBILion data support [download page](https://proteowizard.sourceforge.io/download.html)
+
 <!-- markdown-link-check-enable -->
 
 ## Internet connection
@@ -65,3 +61,32 @@ for spectral networking using MS2Deepscore and DReaMS, an internet connection is
     - https://zenodo.org/ spectral libraries
     - https://external.gnps2.org/gnpslibrary spectral libraries
 <!-- markdown-link-check-enable -->
+
+## Operating system compatibility {#compatibility}
+
+### Windows
+
+Currently, all modules are compatible with Microsoft Windows 10 and higher.
+
+Some libraries for the raw data support for vendor-specific formats are only available for Windows.
+Read more about data support and [data conversion](data_conversion.md).
+
+### Linux
+
+Some libraries for the raw data support for vendor-specific formats are only available for Windows. 
+
+The Linux version **supports** raw data formats from:
+- **Thermo**, **Bruker**, **Waters**
+
+Data from other Vendors may need to be **converted** to the open .mzML format before, including:
+- **Agilent**, **Sciex**, **Shimadzu**, **MOBILion**
+
+### macOS
+
+Some libraries for the raw data support for vendor-specific formats are only available for Windows and Linux. 
+
+The macOS version **supports** raw data formats from:
+- Thermo
+
+Data from other Vendors may need to be **converted** to the open .mzML format before, including:
+- Agilent, Sciex, Shimadzu, MOBILion, Bruker, Waters