Annotator snijderlab
winget install --id=Snijderlab.Annotator -e A simple tool to help you manually discover the depths of your spectra one spectrum at a time. It can load MGF files (only in centroid mode, also do not forget to deconvolute if you have TD data). Once loaded you can select a scan and add you annotation while tweaking the exact settings for generating the annotation. The annotation itself is interactive to help you discover what the spectrum means. Which you can then export as nice images for use in other environments.
Annotator: Professional Spectrum Analysis Tool
Primary Purpose:
Annotator is a tool designed to help manually explore spectra, providing researchers with the ability to delve into complex data sets one spectrum at a time. It supports various file formats and offers interactive features for detailed analysis.
Key Features:
- File Support: Load MGF files in centroid mode and deconvolve TD data. The software also supports mzML, Thermo RAW, Bruker .tdf, and other raw file types.
- Interactive Annotation: Users can select scans, add annotations with precise settings, and interactively explore spectra to enhance understanding.
- Export Capabilities: Generate high-quality images for use in reports or publications.
- Complex Modifications: Supports ProForma 2.0 for complex modifications, including cross-links, chimeric spectra, and glycans.
- Fragmentation Models: Built-in models for HCD, CID, ETD, among others, with options to define custom models.
- Customization: Define custom modifications and models, which can be shared or backed up easily.
Audience & Benefits:
Ideal for researchers in proteomics, glycobiology, and mass spectrometry. Annotator aids in gaining deeper insights into complex spectra through manual annotation, facilitating better understanding of data and enabling the creation of high-quality visualizations for academic and professional use.
Installation:
Available via winget for Windows, ensuring easy setup and integration into your workflow.
Annotator is a comprehensive tool that empowers researchers to explore and understand their spectral data with precision and efficiency.
README
Annotator
A simple tool to help you manually discover the depths of your (complex) spectra, one spectrum at a time. Load your rawfiles, select a spectrum and add your annotation with full control over theoretical fragments. Use the interactive spectrum to discover what your spectrum means and to export gorgeous images.
<img src="images/1_light.svg" />
It can even make nice pictures from glycans as seen below.
<img src="images/2_light.svg" />
Features
> [!TIP] > Do you have some very complex feature in your spectra? It is extremely likely the Annotator can annotate it.
- Open raw files (mgf, mzML, Thermo RAW, Bruker .tdf)
- Full ProForma 2.0 support:
- Complex modifications, from Unimod, PSI-MOD, Resid, and XLMOD, but also masses and formula
- Ambiguous modifications
- Cross-linked peptidoforms
- Chimeric spectra, which includes DIA
- Glycans, both structures and compositions
- Supports complex and highly customizable fragmentation models
- Has built in models for: HCD, CID, ETD, top-down ETD, EtHCD, EtCAD, EAD, EAciD, UVPD
- Supports custom modifications
- Supports loading and searching in 20+ identified peptides file formats
- Amongst others: msFragger, PEAKS, mzTAB, SSL
- Extensive control over the visualisation
- Export to PDF (do not forget to turn on background graphics in the advanced settings while printing)
> [!TIP] > There is also a more comprehensive guide
Peptidoform sequence
It uses the ProForma 2.0 specification to specify the sequence. Here are some examples of valid sequences:
VAEINPSNGGTTFNEKFKGGKATJNormal aminoacidsEM[L-methionine sulfoxide]EVEES[UNIMOD:21]PEKModifications using Unimod and PSI-MODTFNEKF[+15.9949]KGGKATJModifications using raw massesTFNEKF[Formula:O]KGGKATJModifications using elemental formulaTFNEKF[Glycan:HexNAc1Hex2]KGGKATJModifications glycan compositions[+16]-TFNEKFKGGKATJ-[Methyl]Terminal modifications<15N>TFNEKFKGGKATJGlobal isotope modifications (all Nitrogen is 15N)<[S-carboxamidomethyl-L-cysteine]@C>AVYYCSRWGGDGFYAMDYWGQGGlobal modifications (all C are carboxamidomethylated)[UNIMOD:374]?TFNEKFCKGGCKATJModifications where the location is unknownTFNEKFC[UNIMOD:374#g1]KGGC[#g1]KATJ(identical to the one above)TFNEKF(CKGGCK)[UNIMOD:374#g1]ATJ(identical to the one above)VAEINPSNGGTT+FNEKFKGGKATJMultimeric spectra, meaning two separate peptides are in your spectrum at the same timeVAEINK[X:DSSO#XL1]SNGGTT//WAK[#XL1]INKA DSSO cross-link between two lysines on two peptides (note the use of//versus+to indicate cross-linked peptides)VAEINK[X:DSSO#XL1]SNGGTTA hydrolysed DSSO cross-linker
Installing
Using winget
On windows use:
> [!NOTE]
> winget install --id Snijderlab.Annotator.
From binary
See releases for the latest release, here you will also find the prebuilt binaries for your architecture.
From source
To build from source. Clone the repository. And build with cargo tauri dev. Make sure you have installed Rust and Tauri beforehand.
Thermo RAW files
The .NET 8.0 runtime is needed to open Thermo RAW files. Which can be downloaded here. Additionally on windows you can use winget install Microsoft.DotNet.Runtime.8 for a quick install.
Note on custom modifications and models
Custom modifications can be defined, these allow diagnostic ions and neutral losses to be defined. Additionally custom cross-linkers can be defined to have certain cleavage patterns that can then be searched for in the annotator. The custom modifications are stored in a separate json file on your computer. Updating the Annotator will not remove any previously defined modifications. Additionally copying this file to another computer will copy the whole database to that computer. This can be used to move all your definitions to a new computer when upgrading or to aid a colleague with your definitions.
For custom models much of the same is true. These allow highly advanced fragmentation rules to be set. These models will also not be removed when updating and can be shared and backed up in the same way.