OpenMS · tapaswenipathak · May 26, 2022 · May 26, 2022 · May 26, 2022 · May 26, 2022
diff --git a/docs/images/introduction/introduction_LC.png b/docs/images/introduction/introduction_LC.png
diff --git a/docs/images/introduction/introduction_MS.png b/docs/images/introduction/introduction_MS.png
diff --git a/docs/images/introduction/spectrum_peakmap.png b/docs/images/introduction/spectrum_peakmap.png
diff --git a/docs/introduction.md b/docs/introduction.md
@@ -7,21 +7,83 @@ analyses. It offers an infrastructure for rapid development of mass
 spectrometry related software. OpenMS is free software available under the
 three clause BSD license and runs under Windows, macOS, and Linux.
 
-OpenMS has a vast variety of pre-built and ready-to-use tools for proteomics
-and metabolomics data analysis (TOPPTools) as well as powerful 1D, 2D and 3D
-visualization (TOPPView).
-
-OpenMS offers analyses for various quantitation protocols, including label-free
-quantitation, SILAC, iTRAQ, TMT, SRM, SWATH, etc.
-
-OpenMS provides built-in algorithms for de-novo identification and database search,
-as well as adapters to other state-of-the art tools like X!Tandem, Mascot,
-OMSSA, etc. It supports easy integration of OpenMS built tools into workflow
-engines like KNIME, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and
-a unified parameter handling via a 'common tool description' (CTD) scheme.
-
-With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API
-to enable rapid algorithm development. OpenMS supports the Proteomics Standard
-Initiative (PSI) formats for MS data. The main contributors of OpenMS are
-currently the Eberhard-Karls-Universität in Tübingen, the Freie Universität
-Berlin, and the ETH Zürich.
+```{note}
+This introduction is aimed at users new to the field of LC-MS data analysis and will introduce some basics terms
+and concepts. How to handle the data analysis, available data structures, algorithms and more are covered in the various
+subsections of this documentation.
+```
+
+# Background
+
+Proteomics and metabolomics are interdisciplinary research fields that study structure, function, and interaction of
+proteins and metabolites. They employ large-scale experimental techniques that allow acquiring data at the level of
+cellular systems to whole organisms. Mass spectrometry combined with chromatographic separation is commonly used to
+identify, characterize or quantify the amount of proteins and metabolites.
+
+In mass spectrometry-based proteomics and metabolomics, biological samples are extracted, prepared, and separated to
+reduce sample complexity. The separated analytes are ionized and measured in the mass spectrometer. Mass and abundance
+of ions are stored in mass spectra and used to identify and quantify the analytes in the sample using computational
+methods. The quantity and identity of analytes can then be used, for instance, in biomarker discovery, medical diagnostics,
+or basic research.
+
+# 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
+spectrometry-based proteomics, (high-pressure) liquid chromatographic separation techniques (HPLC) are methods of choice
+to achieve a high degree of separation. In HPLC, peptides are separated on a column. Solved in a pressurized liquid
+(mobile phase) they are pumped through a solid adsorbent material (stationary phase) packet into a capillary column.
+Physicochemical properties of each peptide determine how strongly it interacts with the stationary phase. The most
+common HPLC technique in proteomics and metabolomics uses reversed-phase chromatography (RPC) columns. RPC employs a
+hydrophobic stationary phase like octadecyl (C18), a nonpolar carbon chain bonded to a silica base, and a polar mobile
+phase. Polar molecules interact weakly with the stationary phase and elute earlier, while non-polar molecules are retained.
+Interaction can be further modulated by changing the gradient of solvent concentration in the mobile phase over time.
+Elution times in LC are inherently prone to variation, for example, due to fluctuations in the flow rate of the mobile
+phase or change of column. Retention time shifts between runs may be compensated using computational chromatographic
+retention time alignment methods. In the LC-MS setup, the column is directly coupled to the ion source of the mass
+spectrometer.
+
+![](images/introduction/introduction_LC.png)
+
+# 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
+fields.
+
+![](images/introduction/introduction_MS.png)
+
+In a typical mass spectrometer, three principal components can be identified:
+
+- **Ion Source**: A mass spectrometer only handles ions. Thus, charge needs first be transferred to uncharged particles.
+  The component responsible for the ionization is the ion source. Different types of ion sources and ionization
+  techniques exist with electrospray ionization (ESI) being currently the most widely used ionization technique for mass
+  spectrometry-based proteomics.
+
+- **Mass Analyzer**: Most commonly used mass analyzer in proteomics are time-of-flight (TOF) mass analyzers, quadrupole mass
+  filters, and orbitrap analyzers. In TOF mass analyzers, the ions are accelerated in an electric field. The flight time
+  of an ion allows calculating the velocity which in turn is used to calculate the mass-to-charge ratio (m/z). Varying
+  the electric field allows filtering certain mass-to-charge ratios before they enter the detector. In quadrupole mass
+  filters, ions pass through an oscillating electric field created by four parallel rods. For a particular voltage, only
+  ions in a certain mass-to-charge range will reach the detector. The orbitrap is an ion trap mass analyzer (and detector)
+  that traps ions in orbital motion between a barrel-like outer electrode and a spindle-like central electrode allowing
+  for prolonged mass measurement. As a result of the prolonged mass measurements, a high mass resolution can be achieved.
+
+- **Detector**: The last component of the mass spectrometer is the detector. It determines the abundance of ions that
+  passed through the mass analyzer. Ion intensities (a value that relates to its abundance) and the mass-to-charge ratio
+  are recorded in a mass spectrum.
+
+A sample is measured over the retention time of the chromatography typically resulting in tens of thousands of spectra.
+The measurement of one sample is called an MS run and the set of spectra called an MS(1) map or peak map.
+
+![](images/introduction/spectrum_peakmap.png)
+
+The left image displays spectrum with peaks (m/z and intensity values) and the right image shows spectra stacked in
+retention time yielding a peak map.
+
+In proteomics and metabolomics, the MS1 intensity is often used for the quantification of an analyte. Identification
+based on the MS1 mass-to-charge and the isotope pattern is highly ambiguous. To improve identification, tandem mass
+spectrometry (MS/MS) can be applied to assess the analyte substructure. To this end, the precursor ion is isolated and
+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.