MS Annika

<img src="logo/annika_logo.png" align="left" width="175px"/>

MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra.

MS Annika supports identification of protein-protein crosslinks from a variety of different cross-linking reagents, including cleavable and non-cleavable crosslinkers, and various acquisition workflows such as CID/HCD/stepped-HCD MS2 and MS2-MS3 acquisition.

MS Annika features an efficient algorithm for crosslink identification that allows for analysis of proteome-wide studies of both cleavable and non-cleavable crosslinkers on standard computer hardware.

MS Annika comes as user-friendly plugin for the proteomics platform Proteome Discover with a graphical user interface for easy setup and extensive documentation for customization.

You can read more about MS Annika here:

| Description | URL | |:---------------------------|:---------------------------------------------------------------------------------------| | MS Annika 3.0 Publication: | doi.org/10.1038/s42004-024-01386-x | | MS Annika 2.0 Publication: | doi.org/10.1021/acs.jproteome.3c00325 | | MS Annika 1.0 Publication: | doi.org/10.1021/acs.jproteome.0c01000 | | IMP PD Nodes Website: | ms.imp.ac.at/?action=ms-annika |

This repository contains the latest release versions of MS Annika:

| Version | Download URL | |:--------|:-------------| | Latest MS Annika 3.1 version for Proteome Discoverer 3.3 | download | | Latest MS Annika 3.0 version for Proteome Discoverer 3.2 | download | | Latest MS Annika 3.0 version for Proteome Discoverer 3.1 | download | | Latest MS Annika 2.0 version for Proteome Discoverer 3.0 | download | | Latest MS Annika 2.0 version for Proteome Discoverer 2.5 | download | | Latest MS Annika 1.0 version for Proteome Discoverer 2.4 | download | | Latest MS Annika 1.0 version for Proteome Discoverer 2.3 | download |

A list of changes in every version can be found in HISTORY.md.

[!Important] Please note that only MS Annika 3.0 (and above) supports identification of non-cleavable crosslinks and only MS Annika 2.0 (and above) supports identification from MS2-MS3-based acquisition workflows!

Installation

MS Annika is a plug-in for the proteomics software Proteome Discover by Thermo Fisher Scientific. Installation of MS Annika requires:

• Installation of Proteome Discoverer (can be downloaded for free from here)
  • (Requirements of Proteome Discoverer apply)
• Installation of MS Annika via the installer available from this repository
  • There are no additional requirements other than Proteome Discoverer
  • Users will be asked to accept the MS Annika license agreement (MS Annika is licensed as freeware)
  • The typical installation of MS Annika does not take longer than 5 minutes

The tutorial also covers the installation in detail.

Usage

MS Annika makes use of the workflow interface in Proteome Discoverer, which should be straight-forward to use. Step by step instructions for people unfamiliar with Proteome Discoverer are given in the tutorial. The below sections also give an overview of parameters, results, example workflows and example data. Typically an analysis with MS Annika takes a few minutes for small samples and up to a few hours for larger samples and proteome-wide searches. Please also refer to the specific sections for Astral and timsTOF data if you are analyzing such data.

Parameters & Results

Please refer to the MS Annika User Manual for a detailed description of all MS Annika parameters as well as descriptions of all result tables. For further down-stream analysis of MS Annika results we recommend taking a look at MS Annika Extensions.

Tutorial

A tutorial of how to use MS Annika 3.0 can be found here: Text / Video

Example Files

Example files to try MS Annika 3.0 can either be downloaded from PRIDE or directly here:

• Minimal example for a cleavable crosslink MS2 search: MGF + fasta
• RAW file for a non-cleavable crosslink MS2 search: RAW
• RAW file for a cleavable crosslink MS3 search: RAW

Example Workflows

Example workflows that can be used in Proteome Discoverer:

• Proteome Discoverer 3.0 / 3.1 / 3.2 / 3.3:
  • DSS/BS3 MS2 search (CID, ETD, HCD, stepped HCD): pdAnalysis / zip
  • DSS/BS3 MS2 search (for large datasets and proteome-wide searches, CID, ETD, HCD, stepped HCD): pdAnalysis / zip
  • DSSO MS2 search (CID, ETD, HCD, stepped HCD): pdAnalysis / zip
  • DSSO MS2-MS3 search (MS3 recorded in the orbitrap): pdAnalysis / zip
  • DSSO MS2-MS3 search (MS3 recorded in the ion trap): pdAnalysis / zip
  • DSBSO MS2 search (CID, ETD, HCD, stepped HCD): pdAnalysis / zip
  • DSBSO MS2-MS3 search (MS3 recorded in the orbitrap): pdAnalysis / zip
  • DSBSO MS2-MS3 search (MS3 recorded in the ion trap): pdAnalysis / zip
• Proteome Discoverer 2.5:
  • DSSO MS2 search (CID, ETD, HCD, stepped HCD): pdAnalysis / zip
  • DSSO MS2-MS3 search (MS3 recorded in the orbitrap): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw