Mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...

is a scientific technique for measuring the mass-to-charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or

liquid chromatography In chemical analysis, chromatography is a laboratory technique for the separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it through a system ...

and has found widespread adoption in the fields of

analytical chemistry Analytical skill, Analytical chemistry studies and uses instruments and methods to Separation process, separate, identify, and Quantification (science), quantify matter. In practice, separation, identification or quantification may constitute t ...

and

biochemistry Biochemistry, or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology, a ...

where it can be used to identify and characterize

small molecules In molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are small molecules; t ...

and

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

s (

proteomics Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replicatio ...

). The large volume of data produced in a typical mass spectrometry experiment requires that computers be used for data storage and processing. Over the years, different manufacturers of mass spectrometers have developed various proprietary data formats for handling such data which makes it difficult for academic scientists to directly manipulate their data. To address this limitation, several

open Open or OPEN may refer to: Music * Open (band), Australian pop/rock band * The Open (band), English indie rock band * ''Open'' (Blues Image album), 1969 * ''Open'' (Gerd Dudek, Buschi Niebergall, and Edward Vesala album), 1979 * ''Open'' (Go ...

XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing data. It defines a set of rules for encoding electronic document, documents in a format that is both human-readable and Machine-r ...

-based data formats have recently been developed by the

Trans-Proteomic Pipeline The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, Pr ...

at the

Institute for Systems Biology Institute for Systems Biology (ISB) is a non-profit research institution located in Seattle, Washington, United States. ISB concentrates on systems biology, the study of relationships and interactions between various parts of biological systems, ...

to facilitate data manipulation and innovation in the public sector. These data formats are described here.

Open formats

JCAMP-DX

This format was one of the earliest attempts to supply a standardized file format for data exchange in mass spectrometry.

JCAMP-DX JCAMP-DX are text-based file formats created by JCAMP for storing spectroscopic data. It started as a file format for Infrared spectroscopy. It was later expanded to cover Nuclear magnetic resonance spectroscopy, mass spectrometry, electron ma ...

was initially developed for infrared spectrometry. JCAMP-DX is an

ASCII ASCII ( ), an acronym for American Standard Code for Information Interchange, is a character encoding standard for representing a particular set of 95 (English language focused) printable character, printable and 33 control character, control c ...

based format and therefore not very compact even though it includes standards for file compression. JCAMP was officially released in 1988. Together with the

American Society for Mass Spectrometry The American Society for Mass Spectrometry (ASMS) is a professional association based in the United States that supports the scientific field of mass spectrometry. As of 2018, the society had approximately 10,000 members primarily from the US, but ...

a JCAMP-DX format for mass spectrometry was developed with aim to preserve legacy data.

ANDI-MS or netCDF

The Analytical Data Interchange Format for Mass Spectrometry is a format for exchanging data. Many mass spectrometry software packages can read or write ANDI files. ANDI is specified in the ASTM E1947 Standard. ANDI is based on

netCDF NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. The project homepage is hosted by the Unidat ...

which is a software tool library for writing and reading data files. ANDI was initially developed for chromatography-MS data and therefore was not used in the

gold rush where new formats based on

were developed.

AnIML

AnIML is a joined effort of

IUPAC The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of National Adhering Organizations working for the advancement of the chemical sciences, especially by developing nomenclature and terminology. It is ...

and

ASTM International ASTM International, formerly known as American Society for Testing and Materials, is a standards organization that develops and publishes voluntary consensus technical international standards for a wide range of materials, products, systems and s ...

to create an XML based standard that covers a wide variety of analytical techniques including mass spectrometry.

mzData

mzData was the first attempt by the

Proteomics Standards Initiative The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate data comparison, exchange and verification. The Proteomics Standards Initiative focuse ...

(PSI) from the

Human Proteome Organization The Human Proteome Organization (HUPO) is an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. The organization was launched in February 2001, and it promotes ...

(HUPO) to create a standardized format for Mass Spectrometry data. This format is now deprecated, and replaced by mzML.

mzXML

mzXML is a

(eXtensible Markup Language) based common file format for

mass spectrometric data. This format was developed at the Seattle Proteome Center/Institute for Systems Biology while the HUPO-PSI was trying to specify the standardized mzData format, and is still in use in the proteomics community.

YAFMS

Yet Another Format for Mass Spectrometry (YAFMS) is a suggestion to save data in four table relational server-less

database schema The database schema is the structure of a database described in a formal language supported typically by a relational database management system (RDBMS). The term "wikt:schema, schema" refers to the organization of data as a blueprint of how the ...

with data extraction and appending being exercised using

SQL Structured Query Language (SQL) (pronounced ''S-Q-L''; or alternatively as "sequel") is a domain-specific language used to manage data, especially in a relational database management system (RDBMS). It is particularly useful in handling s ...

queries.

mzML

As two formats (mzData and mzXML) for representing the same information is an undesirable state, a joint effort was set by HUPO-PSI, the SPC/ISB and instrument vendors to create a unified standard borrowing the best aspects of both mzData and mzXML, and intended to replace them. Originally called dataXML, it was officially announced as mzML. The first specification was published in June 2008. This format was officially released at the 2008

Meeting, and is since then relatively stable with very few updates. On 1 June 2009, mzML 1.1.0 was released. There are no planned further changes as of 2013.

mzAPI

Instead of defining new file formats and writing converters for proprietary vendor formats a group of scientists proposed to define a common

application program interface An application programming interface (API) is a connection between computers or between computer programs. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how to build su ...

to shift the burden of standards compliance to the instrument manufacturers' existing data access libraries.

mz5

The mz5 format addresses the performance problems of the previous XML based formats. It uses the mzML ontology, but saves the data using the

HDF5 Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large amounts of data. Originally developed at the U.S. National Center for Supercomputing Applications, it is supported by The HDF Group, a non- ...

backend for reduced storage space requirements and improved read/write speed.

imzML

The imzML standard was proposed to exchange data from

mass spectrometry imaging Mass spectrometry imaging (MSI) is a technique used in mass spectrometry to visualize the spatial distribution of molecules, as biomarkers, metabolites, peptides or proteins by their molecular masses. After collecting a mass spectrum at one spot, t ...

in a standardized XML file based on the mzML ontology. It splits experimental data into XML and spectral data in a binary file. Both files are linked by a

universally unique identifier A Universally Unique Identifier (UUID) is a 128-bit label used to uniquely identify objects in computer systems. The term Globally Unique Identifier (GUID) is also used, mostly in Microsoft systems. When generated according to the standard methods ...

mzDB

mzDB saves data in an

SQLite SQLite ( "S-Q-L-ite", "sequel-ite") is a free and open-source relational database engine written in the C programming language. It is not a standalone app; rather, it is a library that software developers embed in their apps. As such, it ...

database to save on storage space and improve access times as the data points can be queried from a

relational database A relational database (RDB) is a database based on the relational model of data, as proposed by E. F. Codd in 1970. A Relational Database Management System (RDBMS) is a type of database management system that stores data in a structured for ...

Toffee

Toffee is an open lossless file format for

data-independent acquisition In mass spectrometry, data-independent acquisition (DIA) is a method of molecular structure determination in which all ions within a selected '' m/z'' range are fragmented and analyzed in a second stage of tandem mass spectrometry. Tandem mass spect ...

mass spectrometry. It leverages

and aims to achieve file sizes similar to those from the proprietary and closed vendor formats.

mzMLb

mzMLb is another take on using a

backend for performant raw data saving. It, however, preserves the mzML XML data structure and stays compliant to the existing standard.

Allotrope

The

Allotrope Foundation The Allotrope Foundation is a consortium of pharmaceutical companies, instrument vendors and software companies to simplify the exchange of scientific electronic data. It publishes the Allotrope Foundation Ontology (AFO) which is a controlled voca ...

curates a

and

Triplestore A triplestore or RDF store is a purpose-built database for the storage and retrieval of triples through semantic queries. A triple is a data entity composed of subject– predicate– object, like "Bob is 35" (i.e., Bob's age measured in years i ...

based file format named Allotrope Data Format (ADF) and a flat

JSON JSON (JavaScript Object Notation, pronounced or ) is an open standard file format and electronic data interchange, data interchange format that uses Human-readable medium and data, human-readable text to store and transmit data objects consi ...

representation ASM short for Allotrope Simple Model. Both are based on the Allotrope Foundation Ontologies (AFO) and contain schemas for mass spectrometry and chromatography coupled with MS detectors.

Proprietary formats

Below is a table of different file format extensions. : (*) Note that the RAW formats of each vendor are not interchangeable; software from one cannot handle the RAW files from another.
(**) Micromass was acquired by Waters in 1997
(***) Finnigan is a division of Thermo

Software

Viewers

There are several viewers for mzXML, mzML and mzData. These viewers are of two types: Free Open Source Software (FOSS) or proprietary. In the FOSS viewer category, one can find MZmine, mineXpert2 (mzXML, mzML, native timsTOF, xy, MGF, BafAscii) MS-Spectre, TOPPView (mzXML, mzML and mzData), Spectra Viewer, SeeMS, msInspect, jmzML. In the proprietary category, one can find PEAKS, Insilicos, Mascot Distiller, Elsci Peaksel. There is a viewer for ITA images. ITA and ITM images can be parsed with the pySPM python library.

Converters

Known converters for mzData to mzXML: :Hermes: A Java "mzData, mzXML, mzML" converter to all directions: publicly available, runs with a graphical user interface, by the Institute of Molecular Systems Biology, ETH Zurich :FileConverter: A command line tool that converts to/from various mass spectrometry formats, part of TOPP Known converters for mzXML: : The Institute for Systems Biology maintains a list of converters Known converters for mzML: :msConvert: A command line tool converting to/from various mass spectrometry formats. A GUI is also available for Windows users. : ReAdW: The Institute for Systems Biology command line converter for Thermo RAW files, part of the TransProteomicPipeline. The latest update of this tool was made in September 2009. Users are now redirected by the TPP development team to use the msConvert software (see above). :FileConverter: A command line tool that converts to/from various mass spectrometry formats, part of TOPP Converters for proprietary formats: :msConvert: A command line tool converting to/from various mass spectrometry formats including multiple proprietary formats. A GUI is also available for Windows users. : CompassXport,

Bruker Bruker Corporation is an American manufacturer of scientific instruments for molecular and materials research, as well as for industrial and applied analysis. It is headquartered in Billerica, Massachusetts, and is the publicly traded parent comp ...

's free tool generating mzXML (and now mzData) files for many of their native file formats (.baf). : MASSTransit, a software to change data between proprietary formats, by Palisade Corporation and distributed by Scientific Instrument Services, Inc and

PerkinElmer PerkinElmer, Inc., previously styled Perkin-Elmer, is an American global corporation that was founded in 1937 and originally focused on precision optics. Over the years it went into and out of several different businesses via acquisitions and di ...

. Purchased from Palisade by John Wiley and Sons in 2020 and incorporated into KnowItAll Spectroscopy softwar
(list of file formats supported).
: Aston, native support for several Agilent Chemstation, Agilent Masshunter and Thermo Isodat file formats : unfinnigan, native support for Finnigan (*.RAW) file formats :

OpenChrom OpenChrom is an Open-source software, open source software for the analysis and visualization of Mass spectrometry, mass spectrometric and Chromatography, chromatographic data. Its focus is to handle native data files from several mass spectrometr ...

, an open source software with support to convert various native file formats including its own open .ocb format to store chromatograms, peaks and identification results Currently available converters are : :: MassWolf, for Micromass MassLynx .Raw format :: mzStar, for SCIEX/ ABI SCIEX/ABI Analyst format :: wiff2dtawiff2dta at sourceforge
/ref> for SCIEX/ ABI SCIEX/ABI Analyst format to mzXML, DTA, MGF and PMF

References

{{reflist Bioinformatics software Mass spectrometry software Proteomics