Merge pull request #4 from carolinelennartsson/main

PTMs

Author: yeroslaviz

MaxSBM.qmd

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+---
+title: "MaxSBM"
+author: "Cox Lab"
+format: 
+  html:
+    toc: true
+    toc-depth: 4
+    toc-expand: false
+    number-sections: true
+    number-depth: 4
+editor: source
+date: today
+bibliography: references.bib
+csl: nature.csl
+---
+
+
+# Sequence based modifications - MaxSBM
+
+To enable the detection of peptides containing sequenced based modifications (SBMs), like SUMOylation and ubiquitination, we configured the software to support sequence-based modifications (SBMs) via the “MaxSBM” module. SBMs are only supported for DDA searches. The module enables identification of PTMs based on multiple fragmentation points.
+
+The module is described in detail in Lennartsson et al., 2025 [@Lennartsson2025-ip]. 
+
+## Configuration 
+The configuration of MaxSBM was implemented through the graphical user interface (GUI). The modification configurations are found in the modification list, under the ‘configuration’ tab (Figure 1.). 
+
+The MaxSBM module can be activated in MaxQuant and Andromeda by incorporating a variable modification in a search with the modification type ‘sequence based modifier’. For SBMs, fragmentation masses are calculated automatically when prompted a sequence input in the ‘sequence’ box, under “Composition” box (Figure 1.).
+
+
+![](images/MaxSBM.png)
+Figure 1. The configurations for including a SBM in a search is done by adding a variable modification with the type “Sequence based modifier” and defining a set of neutral losses and diagnostic ions.  
+
+The PTM remainder masses are defined in the list of neutral losses, which the user can remove add to optimize the search. The ions are denoted p-ions, based on their remaining PTM fragment. The mass is defined based on the fragmentation points neutral mass loss. The ions are numbered based on the p-ion numbering, which is defined in the short name. Here the user can modify and add numbering of the ions. The field can also be left blank, where the ions will be numbered iteratively.  
+
+SBMs generate in general many diagnostic ions. In MaxQuant, adding these will increase the annotation and peak coverage of the data. 
+
+## Search space size 
+Since the number of added p-ions in the neutral loss list increases the search space substantially, we recommend the addition of these to be limited for increased identification rates. 
+
+## Result
+After the search is finished, the identified p-ions are shown in the MaxQuant spectral viewer. The identified p-ions are reported with annotation and mass in the ‘msms.txt’ search output table. The MaxSBM output with the complete set of modification identifications are found in the modification output table ’sites.txt’. We recommend analysis with the downstream proteomics analysis platform Perseus.  
+
+
+![](images/SUMO_spectra.png)
+Figure 2. An example of identified SUMOylated peptide in the MaxQuant viewer.
+
+

PTMs.qmd

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+---
+title: "PTMs - Post Translational Modifications"
+author: "Cox Lab"
+format: 
+  html:
+    toc: true
+    toc-depth: 4
+    toc-expand: false
+    number-sections: true
+    number-depth: 4
+editor: source
+date: today
+bibliography: references.bib
+csl: nature.csl
+---
+
+This page presents an analysis of modifications in MaxQuant, highlighting how they are detected, quantified, and interpreted in proteomic datasets.
+
+
+# Documentation outline
+
+-   PTMs (On this page)
+-   Sequence Based Modifiers in [MaxSBM](MaxSBM.html)
+-   [Analysis with Perseus](modifications.html)
+
+# PTM analysis in MaxQuant
+As a first step towards understanding the complex circuitry of signalling processes, the post-translational modifications (PTMs) should be identified and quantified in an unbiased and global manner. For this purpose, modern quantitative mass spectrometry has proved to be an ideal platform because it is a highly precise yet generic method for detecting PTMs. Despite the impressive progress in MS-based PTM proteomics, exhaustive mapping of protein modifications is challenging for a number of reasons: 
+
+(i) Modified peptides are present in sub-stoichiometric amounts in complex mixtures. 
+(ii) Peptides carrying certain PTMs display more complicated MS/MS fragmentation patterns that can be difficult to interpret.
+(iii) The effective database search space explodes when the search program is allowed to consider potential PTMs at each modifiable amino acid residue.
+(iv) In addition to identifying the modified peptide, the PTM needs to be placed (localized) with single amino acid accuracy in the sequence. 
+
+The talks below will provide an overview of the whole computational PTM proteomics workflow concerned with the identification of modified peptides, localization and occupancy of the identified modifications and generation of quantitative values for modified sites and peptides from the raw data.
+
+# Lectures and tutorials
+
+Lecture - From our 2019 MaxQuant Summer School: 
+
+{{< video https://www.youtube.com/watch?v=fdd9MPt2sAU >}}
+
+Lecture - From our 2024 MaxQuant Summer School 
+
+{{< video https://www.youtube.com/watch?v=sbhoDTEueUk >}}
+
+Lecture - From our 2024 MaxQuant Summer School 
+
+{{< video https://www.youtube.com/watch?v=kuhKel803xk >}}
+
+Tutorial - From our 2024 MaxQuant Summer School 
+
+{{< video https://www.youtube.com/watch?v=SXfYl6lh324 >}}
+
+Lecture -From our 2025 MaxQuant Summer School 
+
+{{< video https://www.youtube.com/watch?v=QWF4afyPv-o >}}
+
+
+
+
+