Spectroscopy file formats from 1988 to today

A spectrum is measured data, not structure: intensities along an axis, or a list of peaks. A format for spectra has to store the numbers with their acquisition parameters and link them to the compound they describe. This post covers the open formats in the order they appeared.

A short history#

JCAMP-DX, 1988#

JCAMP-DX was published in 1988 for infrared spectra and later extended to NMR, mass spectra, UV-Vis and Raman; IUPAC now maintains it.¹ A file is plain text: labelled records that begin with ##, then the data, as in this spectrum from the NIST/Coblentz collection:

##TITLE=ETHANOL
##JCAMP-DX=4.24
##DATA TYPE=INFRARED SPECTRUM
##CAS REGISTRY NO=64-17-5
##STATE=GAS
##XUNITS=1/CM
##YUNITS=TRANSMITTANCE
##NPOINTS=3570
##XYDATA=(X++(Y..Y))
461.563000 0.9660 0.9660 0.9660 0.9660 0.9660
466.250502 0.9680 0.9680 0.9680 0.9680 0.9680

(X++(Y..Y)) means that each line gives an x value followed by y values at a fixed spacing. Compressed variants encode digits, differences and repeats as letters, and a linked block can hold the structure.

ANDI and mzData#

For chromatography and mass spectrometry, ANDI (1995) stored data in binary netCDF, and mzData (2003), from the Proteomics Standards Initiative, moved to XML.

mzML, 2008#

mzML merged mzData and mzXML into one standard.² Instrument settings and scan properties are named by terms from a controlled vocabulary, and spectra are stored as base64-encoded binary arrays. ProteoWizard converts most vendor formats to it. For imaging mass spectrometry, imzML keeps the metadata in XML and the spectra in a separate binary file.³

AnIML#

The Analytical Information Markup Language, developed under ASTM subcommittee E13.15, aims to hold any analytical technique in one XML schema, so that an HPLC run with UV and MS detection fits in one file. It is not yet a final standard.⁴

nmrML, 2017#

nmrML does for NMR what mzML does for mass spectra.⁵ It stores the raw FID, the acquisition parameters, the processed spectrum and, where available, the assigned structure. Converters exist for Bruker, JEOL and Agilent data, and the MetaboLights repository stores NMR data in it.

NMReDATA, 2018#

NMReDATA stores the NMR parameters of an assigned structure as data items in an SD file: shifts, integrals, multiplicities, coupling constants and 2D correlations, under tags such as NMREDATA_ASSIGNMENT.⁶ Any program that reads SD files, described in Cheminformatics file formats, can read the structure.

Side by side#

On this site#

The spectrum file converter reads JCAMP-DX, SPC, CSV and XY files and exports CSV, JSON, JCAMP-DX or Excel. Signum opens NMR, IR, UV-Vis and mass spectra for peak picking and integration, and the NMR predictor estimates ¹H and ¹³C shifts from a structure. Line notations are covered in Chemistry line notations.

References#

1. McDonald RS, Wilks PA. JCAMP-DX: a standard form for exchange of infrared spectra in computer readable form. Appl. Spectrosc. 42, 151–162 (1988). doi:10.1366/0003702884428734
2. Martens L et al. mzML: a community standard for mass spectrometry data. Mol. Cell. Proteomics 10, R110.000133 (2011). doi:10.1074/mcp.R110.000133
3. Schramm T et al. imzML: a common data format for the flexible exchange and processing of mass spectrometry imaging data. J. Proteomics 75, 5106–5110 (2012). doi:10.1016/j.jprot.2012.07.026
4. AnIML, ASTM subcommittee E13.15. animl.org
5. Schober D et al. nmrML: a community supported open data standard for the description, storage, and exchange of NMR data. Anal. Chem. 90, 649–656 (2018). doi:10.1021/acs.analchem.7b02795
6. Pupier M et al. NMReDATA, a standard to report the NMR assignment and parameters of organic compounds. Magn. Reson. Chem. 56, 703–715 (2018). doi:10.1002/mrc.4737