Importing data

The load function reads a mass spectrometry file and returns a Vector{MSscan}. The file format is automatically determined from the extension.

Supported file formats: mzXML, mzML, MGF, MSP, imzML, TXT.

julia> scans = load("test.mzXML")
6-element Array{MassJ.MSscan,1}:
 MassJ.MSscan(1, 0.1384, 5.08195e6, ...)
...

julia> scans = load("test.mzML")
3-element Array{MassJ.MSscan,1}:
 MassJ.MSscan(1, 0.5, 19000.0, ...)
...

julia> scans = load("test.mgf")
3-element Array{MassJ.MSscan,1}:
 MassJ.MSscan(1, 0.5, 4800.0, ...)
...

julia> scans = load("library.msp")
3-element Array{MassJ.MSscan,1}:
 MassJ.MSscan(1, 0.0, 178600.0, ...)
...

julia> scans = load("sample.imzML")
10000-element Array{MassJ.MSscan,1}:
 MassJ.MSscan(1, 0.0, 8000.0, ...)
...

Individual scans may be retrieved from the array the usual way:

julia> scans[1]
MassJ.MSscan(1, 0.1384, 5.08195e6, ...)

julia> scans[1].mz
22320-element Array{Float64,1}:
 140.083
 ...

Format-specific notes

mzXML

The mzXML reader supports both 32-bit and 64-bit precision data, zlib compression, and nested scan hierarchies (MS1 → MS2 → MS3).

The mzML reader supports the PSI (Proteomics Standards Initiative) standard format. It handles both indexedmzML and raw mzML files. Binary data arrays are decoded from base64 with optional zlib compression in little-endian byte order. Retention times are automatically converted to minutes regardless of the unit in the file (minutes or seconds). Ion mobility metadata (drift time, 1/K0, compensation voltage) is extracted when present.

MGF

The MGF (Mascot Generic Format) reader loads centroided peak lists. Each BEGIN IONS...END IONS block becomes one MSscan. The PEPMASS field sets the precursor m/z, CHARGE sets the charge state, and RTINSECONDS is converted to minutes. The TITLE and original SCANS values are stored in the metadata dictionary.

MSP

The MSP reader loads spectra from NIST Mass Spectral Library files used by NIST, MoNA, MassBank, and GNPS. Each entry starts with Name: and contains metadata fields (e.g. Precursor_mz, Ion_mode, Collision_energy, Formula, InChIKey) followed by Num Peaks: and the peak list. Both one-pair-per-line and semicolon-separated formats are supported. Rich metadata (name, formula, MW, InChIKey, CAS#, DB#, precursor type, comments) is stored in the metadata dictionary of each scan.

imzML

The imzML reader loads imaging mass spectrometry data. The format consists of an XML metadata file (.imzML) following the mzML schema with IMS-specific CV terms for spatial coordinates, and a companion binary data file (.ibd) in the same directory. Both continuous and processed storage modes are supported. Spatial coordinates (x, y, and optionally z) are stored in the metadata dictionary as "position_x", "position_y", and "position_z". The info function also reports image dimensions. Binary data supports 32-bit and 64-bit precision with optional zlib compression.

TXT

The TXT reader loads a single spectrum from a two-column whitespace-separated file (m/z and intensity).

Chromatograms

Chromatograms may be retrieved from a file and imported in MassJ.Chromatogram:

julia> chromatogram("test.mzML")
MassJ.Chromatogram([0.5, 1.0, 1.5], [19000.0, 4800.0, 2100.0], 19000.0)

Retention time

The function MassJ.retention_time reads the retention times from a file and returns a Vector{Float64} in minutes.

julia> MassJ.retention_time("test.mzML")
3-element Array{Float64,1}:
  0.5
  1.0
  1.5