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v3.0.5
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michabirklbauer authored Dec 2, 2024
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# History

## MS Annika 3.0 v3.0.5

- Release date: 2. December 2024
- Supported Proteome Discoverer versions: 3.1
- Changes:
- Minor:
- Several memory optimizations to better deal with Astral data
- Removed experimental rescoring feature for non-cleavable crosslinks

## MS Annika 3.0 v3.0.2

- Release date: 18. June 2024
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## 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](#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.
unfamiliar with Proteome Discoverer are given in the [tutorial](#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

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This workflow additionally requires the installation of the [IMP MS2 Spectrum Processor](https://ms.imp.ac.at/?action=spectrum-processor) node beforehand, which can be directly downloaded from [here (Proteome Discoverer 3.0)](https://ms.imp.ac.at/?file=spectrum-processor/ms2spectrumprocessor_3.0.zip).

## Support for Astral Data

In order to process crosslinking data from Astral instruments we recommend using [MS Annika 3.0 v3.0.5](https://github.com/hgb-bin-proteomics/MSAnnika/releases/tag/v3.0.5) or greater (e.g. [**latest**](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zip)). Although theoretically all MS Annika versions support Astral data, earlier versions require sufficient hardware for processing RAW files of more than 100 000 spectra (specifically enough memory, 128GB+ is recommended). MS Annika version 3.0.5+ is memory optimized and runs on standard commodity hardware. We also recommend disabling the following parameter:

- MS Annika Detector Node:
- Doublet Selection:
- Try infer missing charge states: False (If this parameter is not visible, please check that `Show Advanced Parameters` is on).

## Support for MGF and timsTOF Data

The following MS Annika versions support MGF\* and timsTOF\*\* data input:
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MS Annika 3.0 version 3.0.5
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MS Annika 3.0 version 3.0.2
MS Annika 3.0 version 3.0.5

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