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Mass spectrometry was long considered a specialist technology for physicists and chemists, but is now used across biological research. Two major driving forces of this development are Electrospray Ionization and the Orbitrap mass analyzer. On the occasion of their 30th and 20th anniversaries in 2019, we assembled this collection of Nature Communications articles.
The sections Protein Mass Spectrometry and Beyond Proteins feature applications of Electrospray Ionization- and Orbitrap-based mass spectrometry. The Opinion and Reviews section is continuously updated with Editorials, Commentaries, Perspectives and Reviews on various topics in biological mass spectrometry. As the advances of mass spectrometry are closely connected to the emergence of proteomics, we added a section on The Human Proteome in 2020 to celebrate 10 years of the Human Proteome Project.
Originally designed for measuring isotope abundances and elemental masses, mass spectrometry is becoming a mainstay across life sciences. As electrospray ionization of biomolecules turns 30 and the Orbitrap mass analyzer 20, we take this opportunity to highlight the role of both inventions in stirring mass spectrometry from physics into biology and discuss the advances and challenges that may impact the future applications of biomolecular mass spectrometry.
John Fenn’s electrospray mass spectrometry (ESMS) was awarded the chemistry Nobel Prize in 2002 and is now the basis of the entire field of MS-based proteomics. Technological progress continues unabated, enabling single cell sensitivity and clinical applications.
The establishment of the Orbitrap analyzer as a major player in mass spectrometry based proteomics is traced back to the first public presentation of this technology 20 years ago; when a proof-of-principle application led the way to further advancements and biological applications.
Lack of best practice guidelines currently limits the application of metabolomics in the regulatory sciences. Here, the MEtabolomics standaRds Initiative in Toxicology (MERIT) proposes methods and reporting standards for several important applications of metabolomics in regulatory toxicology.
Glycomics is gaining momentum in basic, translational and clinical research. Here, the authors review current reporting standards and analysis tools for mass-spectrometry-based glycomics, and propose an e-infrastructure for standardized reporting and online deposition of glycomics data.
The Human Proteome Project (HPP) was launched in 2010 to enhance accurate annotation of the genome-encoded proteome. Ten years later, the HPP releases its first blueprint of the human proteome, annotating 90% of all known proteins at high-stringency and discussing the implications of proteomics for precision medicine.
More and more clinical studies include potentially sensitive human proteomics or metabolomics datasets, but bioinformatics resources for managing the access to these data are not yet available. This commentary discusses current best practices and future perspectives for the responsible handling of clinical proteomics and metabolomics data.
The number of publicly available proteomics datasets is growing rapidly, but a standardized approach for describing the associated metadata is lacking. Here, the authors propose a format and a software pipeline to present and validate metadata, and integrate them into ProteomeXchange repositories.