Mass Spectrometry (MS) is finding new users every day. As experience and insights are growing, new types of applications rapidly emerge. A problem is the multitude of data and file formats, hence this article is focused on formats and analytical topics.

Overview

Mass Spectrometry software is very complex. Many software suites are proprietary and limited to specific types of applications. There are some standards covering certain aspects in the sequence from equipment configuration and data acquisition through transfer, storage, analysis and result representation (on-screen or printed document).

MS Technology

Mass spectrometry (MS) includes analysis techniques to identify and quantify biological and chemical compounds which create a molecular fingerprint. It includes preparing and normalizing data, calibration of spectra and searching for statistically meaningful peaks in the samples.

There are three basic parts in a mass spectrometer:

• ion source: transforms the molecules in a sample into ionized fragments
• mass analyzer: electric and magnetic fields sort the ions by their masses
• detector: measures and calculates the abundances of each ion fragment type
• with a great variety of devices and analytical techniques each with its own set of requirements, data formats and problems.

Software

MS equipment is of great functional and physical variety. There are many different proprietary and ‘to be' standardized data formats. Analytical chemistry, and especially mass-spectrometry is critically dependent on optimal instrumentation and a correct interpretation of the raw data. Hence, raw data should be compared with known spectra from libraries of reference spectra and the data must be processed correctly. Robust algorithms have to be thoroughly tested to eliminate potential flaws. Each type of mass spectrometer is optimized for specific methods of ionization and detection, based on incompatible data formats and lack of infrastructure to handle mass spectrometry data. Because of this, researchers have to use the software tools bundled with each mass spectrometer, this complicates database construction and makes comparisons between results from different mass spectrometers difficult.

The proprietary nature of the software tools limits the users who want to modify these tools for their individual needs.

Data/File Format Standards

Development in instrumentation and computing equipment is progressing very fast. This creates the problem that the hardware and software environment used to retrieve data for analysis will be different from that which was used to create it. To preserve the content of the original data, a data storage format must be:

• based on open data format standards
• readable for 20 to 30 years because of regulatory compliance and patent protection
• usable through changes in computer hardware/software, operating systems and storage media
• able to precisely represent the original data to meet regulatory requirements
• able to recognize data from a variety of instruments, extensible for new types and backwards compatible

Many existing data standards are specific to certain instrumentation. Some organizations have opted not to use the existing data storage standards at all, but instead store graphical representations of a final report. Hence, the content of the archived file is restricted to the data included in the original report. The graphics are of no use, if a regulatory inspector needs to view associated information that was not incorporated in the report.

The public XML standard has features that seem to make it ideal as the basis of a file format for long-term storage and access for instrument data. One of the features of XML is that it has been developed completely in the public domain by the World Wide Web Consortium. XML is not actually a file format, but is a standardized, application-independent way of representing data using plain ASCII text. In contrast to unstructured ASCII documents, XML has an inherent system of defining hierarchical tags and attributes that describe the relationships between pieces of data. This tagging makes it possible to extend and combine XML data structures without reformatting the information. It addresses all of the critical requirements listed below:

• ASCII storage mechanism, which is human readable, now and in the future
• ASCII files are easy to migrate to any operating system, hardware/software platform and storage media
• based on a public domain standard controlled by a completely independent body
• describes and shares complex data structures via the use of public-domain XSDs
• can encapsulate binary information to maintain numerical accuracy using standard ASCII characters
• designed to be extensible while backwards compatible

One drawback of XML data representation is that the data set size can be larger than a proprietary binary format containing the same information by a factor of 2 to 3. Today's low cost of storage media and lossless compression technologies make this a minor issue.