MS Annika

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

You can read more about MS Annika here, here and here.

This repository contains the latest release versions of MS Annika.

• Latest MS Annika 2.0 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 version for Proteome Discoverer 2.4: download
• Latest MS Annika version for Proteome Discoverer 2.3: download

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

Tutorial

A tutorial of how to use MS Annika 2.0 can be found here: Text / Video

Example Files

Example files to try MS Annika 2.0 can either be downloaded from PRIDE or directly here:

• Minimal example for MS2 search: MGF + fasta
• RAW file for MS3 search: RAW

Example Workflows

Example workflows that can be used in Proteome Discoverer:

• Proteome Discoverer 3.0 / 3.1:
  • 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 / zip
  • DSSO MS2-MS3 search (MS3 recorded in the ion trap): pdAnalysis / zip

The provided workflows also require the installation of MS Amanda which can be downloaded here.

The general processing workflow for almost any crosslink search is depicted here.

For MS2 searches (CID, ETD, HCD, stepped HCD) it can also be beneficial to employ the IMP MS2 Spectrum Processor node, an example workflow for Proteome Discoverer 3.0 is given here:

• DSSO MS2 search with IMP MS2 Spectrum Processor: pdAnalysis / zip

This workflow additionally requires the installation of the IMP MS2 Spectrum Processor node beforehand, which can be directly downloaded from here.

Support for MGF and timsTOF Data

The following MS Annika versions support MGF* and timsTOF** data input:

• Proteome Discoverer 3.1: MS Annika 2.0 v2.2.1
• Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4fix
• Proteome Discoverer <=2.5: MS Annika 1.0 v1.0.0***

*MS Annika 2.0 only supports MS2 search for MGF files since MGF files don't contain sufficient MS3 information.
**requires installation of the Bruker Ion Mobility reader.
***requires installation of the IMP MS2 Spectrum Processor node.

Known Issues

List of known issues

Citing

If you are using MS Annika please cite:

MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity
Micha J. Birklbauer, Manuel Matzinger, Fränze Müller, Karl Mechtler, and Viktoria Dorfer
Journal of Proteome Research 2023 22 (9), 3009-3021
DOI: 10.1021/acs.jproteome.3c00325

or

MS Annika: A New Cross-Linking Search Engine
Georg J. Pirklbauer, Christian E. Stieger, Manuel Matzinger, Stephan Winkler, Karl Mechtler, and Viktoria Dorfer
Journal of Proteome Research 2021 20 (5), 2560-2569
DOI: 10.1021/acs.jproteome.0c01000

Contact

• micha.birklbauer@fh-hagenberg.at