MassJ.jl

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A mass spectrometry package for Julia

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<p align="center">
  <h1 align="center"> MassJ.jl  </h1>
</p>
<p align="center">
  <img align="center" src="docs/src/assets/logo.png" width="400" height="200" />
</p>
<p align="center">
  <normal> A mass spectrometry package for Julia </normal>
</p>

##
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[![Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://ajgiuliani.github.io/MassJ.jl/stable)
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## What MassJ does

MassJ.jl is a general-purpose Julia package for loading, processing, and
analysing mass spectrometry data. It is designed to slot into the rest of the
Julia ecosystem (Plots.jl, Statistics, DataFrames) rather than to replicate
the feature surface of pipelines like OpenMS or pyteomics.

- **Read & write open formats** — mzML (incl. indexed-mzML), mzXML, MGF, MSP,
  imzML, plain TXT. mzML output is PSI 1.1.0 schema-validated and accepted by
  MaxQuant and other downstream tools.
- **Signal processing** — Savitzky-Golay smoothing, centroiding (SNRA,
  template-based peak detection, continuous wavelet transform), baseline
  correction (TopHat, LOESS, IPSA).
- **Isotopes & deconvolution** — chemical-formula parsing, exact/average/
  nominal masses, isotopic distribution simulation, UniDec-style charge-state
  deconvolution.
- **Energy-resolved yields** — purpose-built pipeline for UVPD / action
  spectroscopy / CID breakdown: locate peaks, integrate per scan, propagate
  proper per-scan errors, normalize by TIC and/or photon flux, plot with
  uncertainty ribbons.
- **Native plots** — Plots.jl recipes for spectra, chromatograms, and yield
  curves out of the box.

## Installation

```julia
julia> ]
pkg> add MassJ
```

## Quick start

```julia
using MassJ, Plots

scans = load("input.mzML")               # → MSrun (a Vector{MSscan} + file metadata)
avg   = average(scans, Level(1))         # average all MS1 spectra
clean = baseline_correction(smooth(avg)) # SG smooth + TopHat baseline
plot(clean)                              # one-line plot

# Save back (indexed mzML by default; MaxQuant-compatible)
save(clean, "processed.mzML")
```

A more substantial workflow — energy-resolved yields for action-spectroscopy
data:

```julia
peaks = [Peak(110.5, "fragment_a"; tol = 0.5),
         Peak(500.05, "precursor"; ppm = 5.0)]

yc = yields("data/UVPD/", peaks; x0 = 3.0, step = 0.1,
            xlabel = "photon energy (eV)")
yc = yc |> normalize_tic |> y -> normalize_flux(y, "flux.txt")

plot(yc)                                 # ribbons show per-scan SEM
write_csv(yc, "yields.csv")
```

## Documentation

Full documentation is at
[ajgiuliani.github.io/MassJ.jl](https://ajgiuliani.github.io/MassJ.jl/stable).
The manual covers each format, the processing pipeline, the yields workflow,
and the reference API.

## Supported file formats

| Format | Read |    Write     |
|--------|:----:|:------------:|
| mzML   |  ✅  | ✅ (indexed) |
| mzXML  |  ✅  |      ✅      |
| MGF    |  ✅  |      ✅      |
| MSP    |  ✅  |      ✅      |
| imzML  |  ✅  |      ✅      |
| TXT    |  ✅  |      ✅      |

## Citing

If you use MassJ in published work, please cite it via the [CITATION.cff](CITATION.cff) metadata at the repository root.

The deconvolution, isotopic-distribution, and wavelet peak-detection routines
are independent re-implementations of published algorithms, and the imzML
reader adapts third-party MIT-licensed code — please also cite the original
work (license notices are in [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md)):

* **IsoSpec** (isotopic distributions): Łącki, M. K.; Startek, M.;
  Valkenborg, D.; Gambin, A. *IsoSpec: Hyperfast Fine Structure Calculator.*
  Anal. Chem. **2017**, 89, 3272.
  [Project](https://github.com/MatteoLacki/IsoSpec)
* **CWT peak detection** (continuous wavelet transform centroiding): Du, P.;
  Kibbe, W. A.; Lin, S. M. *Improved peak detection in mass spectrum by
  incorporating continuous wavelet transform-based pattern matching.*
  Bioinformatics **2006**, 22, 2059.
  DOI: [10.1093/bioinformatics/btl355](https://doi.org/10.1093/bioinformatics/btl355).
* **UniDec** (charge/mass deconvolution): Marty, M. T.; Baldwin, A. J.;
  Marklund, E. G.; Hochberg, G. K. A.; Benesch, J. L. P.; Robinson, C. V.
  *Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary
  Interactions to Polydisperse Ensembles.* Anal. Chem. **2015**, 87, 4370.
  DOI: [10.1021/acs.analchem.5b00140](https://doi.org/10.1021/acs.analchem.5b00140).
  [Project](https://github.com/michaelmarty/UniDec)
* **julia_mzML_imzML** (imzML streaming reader): the DOM-free imzML reader in
  `src/imzml_stream.jl` adapts the streaming-parse strategy of julia_mzML_imzML
  by R. Winkler (MIT-licensed). Rosas-Román, I.; Guillén-Alonso, H.;
  Moreno-Pedraza, A.; Winkler, R. *Open-source data processing for imaging mass
  spectrometry.* Anal. Chem. **2024**.
  DOI: [10.1021/acs.analchem.3c05853](https://doi.org/10.1021/acs.analchem.3c05853).
  [Project](https://codeberg.org/LabABI/julia_mzML_imzML)

## Related Julia packages

* [MzXML.jl](https://github.com/timholy/MzXML.jl) — older mzXML loader
* [julia_mzML_imzML](https://codeberg.org/LabABI/julia_mzML_imzML) — fast mzML & imzML reader / imaging MS
* [MassSpec.jl](https://gitlab.com/odurif/MassSpec.jl) — assorted MS utilities

## Contributing

Issues and pull requests are welcome — see [CONTRIBUTING.md](CONTRIBUTING.md)
for the workflow.

## License

GPL-3.0-or-later, see [LICENSE](LICENSE).

**License history.** MassJ.jl was released under CeCILL-C from its first public
version through v0.3.1 (2019). From v1.0.0 (2026-04-10) onward it is licensed
under GPL-3.0-or-later. Earlier tagged releases remain available under CeCILL-C
through the git history.

MassJ.jl

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