EDITORIAL OPEN The path of biomolecular mass spectrometry into open research

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.

he rate of scientific discovery is into the biology limelight with a review article often dramatically accelerated by published in 19892. Ten years later, Alex-

1234567890():,; new methodological approaches ander Makarov introduced the Orbitrap mass Tor instruments. A few examples analyzer, presenting a new approach enabling immediately come to mind: X- robust mass measurements at high resolu- ray crystallography enabled the visualiza- tion3. Although it was not until 2005 that a tion of proteins in three-dimensional commercial Orbitrap mass spectrometer space; massively parallel sequencing trans- became available, Makarov’s presentation in formed the fields of genomics, tran- 1999 provided the first glimpse into the scriptomics and epigenetics by increasing underlying principles of what is today one of throughput and decreasing sequencing themostwidelyusedmassanalyzersfor costs by orders of magni- proteomics and analytical chemistry. “… as the demands for data tude; and CRISPR-Cas To highlight the anniversaries of these two now allows genetic key enabling advances in the life sciences, we and method transparency manipulations to be car- recently unveiled a collection of articles continue to increase, all ried out with a level of published in Nature Communications that speed and accuracy that showcases applications of ESI- and Orbitrap- areas of mass spectrometry would have qualified as mass spectrometry in the life and clinical science fiction a mere 10 sciences. The collection features recent applications are challenged years ago. 2019 marks the research, review and perspective articles, as with regard to decennial anniversaries of well as papers that have attracted our read- two such innovations in ers’ attention over several years. It covers standardization of analytical the application of mass proteomics, approaches to localize and spectrometry that have quantify post-translational modifications, workflows and data sharing.” transformed several fields mass spectrometry-based structural biology, of biological and clinical and mass spectrometric analyses of other research: electrospray ionization of large biomolecules such as carbohydrates, nucleic biomolecules, and their high-resolution acids and metabolites. In two historical detection with the Orbitrap mass analyzer. perspectives, the Orbitrap inventor Alex- Electrospray ionization (ESI) was originally ander Makarov recounts how this mass described in 1984 by the 2002 Nobel laureate analyzer came into being and Matthias John B. Fenn and his colleague Masamichi Mann, John Fenn’s graduate student and Yamashita1; who showed that inserting an one of the first researchers to analyze pro- aqueous sample solution in a conductive teinsbymassspectrometry2,revisitsthe capillary and applying an electrical current invention of ESI and the subsequent emer- allows generating gaseous ions of the sample gence of proteomics4,5. compounds that can be measured by mass Notwithstanding the importance of spectrometry. Following the demonstration ESI and the Orbitrap analyzer, there that ESI enables the mass spectrometric are many other influential developments analysis of labile biomolecules, Fenn and his that paved the way towards biological coworkers brought ESI-mass spectrometry mass spectrometry (www.nature.com/

NATURE COMMUNICATIONS | (2019) 10:4029 | https://doi.org/10.1038/s41467-019-12150-4 | www.nature.com/naturecommunications 1 EDITORIAL NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-12150-4 milestones/mass-spec). As both Mann5 and also raise expectations. At Nature Com- References Makarov4 point out, key elements of state-of- munications, we expect biological and 1. Yamashita, M. & Fenn, J. B. Electrospray ion the art mass spectrometers were invented clinical studies that use mass spectrometry source. Another variation on the free-jet theme. J. Phys. Chem. 88, 4451–4459 (1984). long before the application of mass spectro- to thoroughly validate discovery phase 2. Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F. & metry to biomolecules. Following the works results and demonstrate their physiological Whitehouse, C. M. Electrospray ionization for of the physicists Joseph John (J.J.) Thomson relevance. Similarly, studies describing new mass spectrometry of large biomolecules. Science and Wilhelm Wien on positive rays and or improved mass spectrometry methods 246,64–71 (1989). cathode rays6,7, mass spectrometry arose as and workflows must stand up to rigorous 3. Makarov, A. The Orbitrap: a novel high- fi performance electrostatic trap. in Proceedings of an analytical technique that was rst applied benchmarking against existing approaches the 47th ASMS Conference on Mass Spectrometry to measuring stable elemental isotopes in the and provide compelling proof-of-concept and Allied Topics, Dallas, Texas (1999). gas phase8. Owing to the development of applications. Concomitantly, as the 4. Makarov, A. Orbitrap journey: taming the ion additional methods to ionize and fragment demands for data and method transpar- rings. Nat. Commun. 10, https://doi.org/10.1038/ analytes, new mass analyzers to measure ency continue to increase, all areas of mass s41467-019-11748-y (2019). 5. Mann, M. The ever expanding scope of their mass-to-charge ratios, and increasingly spectrometry applications are challenged electrospray mass spectrometry – a 30 year comprehensive compound libraries, mass with regard to standardization of analytical journey. Nat. Commun. 10, https://doi.org/ spectrometry soon became an established workflows and data sharing. Mass spec- 10.1038/s41467-019-11747-z (2019). tool in chemical research. However, mass trometry users have made significant 6. Thomson, J. J. X.L. Cathode Rays. Lond. Edinb. 44 – spectrometric analysis of proteins and nucleic headway in addressing these issues by Dubl. Philos. Mag. , 293 316 (1897). 7. Wien, W. Untersuchungen über die elektrische acids remained out of reach because their proposing best practice guidelines for var- Entladung in verdünnten Gasen. Ann. Phys. 310, more labile peptide or sugar-phosphate ious disciplines and by improving the 421–435 (1901). backbones were lost during the transfer into online data repositories, yet several hurdles 8. Aston, F. W. Isotopes and Atomic Weights. the gas phase. This changed— allowing mass remain. Reproducible protocols and stan- Nature 105, 617–619 (1920). spectrometry to enter the realm of biology— dardized data reporting—still not uni- 9. Karas, M. & Hillenkamp, F. Laser desorption 2 ionization of proteins with molecular masses with the invention of ESI , where charged versally embraced in fundamental exceeding 10,000 daltons. Anal. Chem. 60, droplets of sample solution gradually deso- biological mass spectrometry—become 2299–2301 (1988). lvate until only ‘naked’ molecular ions essential when analyzing and comparing 10. Tanaka, K. et al. Protein and polymer analyses up remain; and matrix-assisted laser desorption/ large cohorts of samples. Depositing mass to m/z 100 000 by laser ionization time-of-flight ionization (MALDI)9,10,whichrelieson spectral raw data to publically accessible mass spectrometry. Rapid Commun. Mass Spectrom. 2, 151–153 (1988). embedding biomolecules in an energy- repositories remains to become the norm 11. Schwamborn, K. & Caprioli, R. M. Molecular absorbing crystalline matrix ionized with a outside of proteomics, which is partially imaging by mass spectrometry—looking beyond laser pulse of appropriate energy and attributable to the fact that suitable com- classical histology. Nat. Rev. Cancer 10, 639–646 wavelength. munity repositories are still lacking. (2010). While the majority of biological mass Beyond expanding standardized raw data 12. Oviaño, M. & Bou, G. Matrix-assisted laser desorption ionization-time of flight mass spectrometry applications today rely on repositories, mass spectrometry-based spectrometry for the rapid detection of ESI, MALDI remains widely used to clinical research calls for data sharing antimicrobial resistance mechanisms and beyond. visualize the spatial distribution of mole- workflows that provide access to the data Clin. Microbiol. Rev. 32, e00037-18 (2019). cules in histological mass spectrometry without compromising patient con- 13. Zhang, B. et al. Clinical potential of mass imaging experiments11 and for the rapid fidentiality and without requiring reviewers spectrometry-based proteogenomics. Nat. Rev. fi Clin. Oncol. 16, 256–268 (2019). identi cation of microorganisms in clinical and other researchers to reveal their iden- 14. Magnani, R., Dirk, L. M. A., Trievel, R. C. & Houtz, 12 microbiology . These and other recent tity to the study lead. R. L. Calmodulin methyltransferase is an developments13 illustrate how the applica- For both new applications and metho- evolutionarily conserved enzyme that trimethylates tion of mass spectrometry has expanded dological advances in mass spectrometry, it Lys-115 in calmodulin. Nat. Commun. 1, 43 (2010). from physics into chemistry, biology and is increasingly clear that their full potential 15. Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and even clinical research. Being relevant to so will be realized only if methods, data, code, stewardship. Sci. Data 3, 160018 (2016). many disciplines, mass spectrometry based and software are reported in accordance 16. Kim, M.-S. et al. A draft map of the human research finds a natural home within Nat- with the community guidelines and made proteome. Nature 509, 575–581 (2014). ure Communications. A study applying findable, accessible, interoperable, and reu- 17. Wilhelm, M. et al. Mass-spectrometry-based draft of 509 – mass spectrometry to discover a protein sable (FAIR15). On its way to becoming a the human proteome. Nature , 582 587 (2014). methyltransferase was published within FAIR research field, biomolecular mass our first 50 articles14 and we have since spectrometry must overcome the obstacles fi Open Access This article is licensed then been striving to publish signi cant outlined above, which will require concerted under a Creative Commons Attribution advances in all areas of mass spectrometry. efforts from all parties involved in the sci- 4.0 International License, which permits use, sharing, Since Nature Communications’ first entific process. This presents a formidable adaptation, distribution and reproduction in any medium mass spectrometry paper, the field has challenge, but it is well worth the effort. As or format, as long as you give appropriate credit to the continued to evolve. Mass spectrometers 2019 also marks the fifth anniversaries of original author(s) and the source, provide a link to the and data analysis tools have become sub- the human proteome drafts—two landmark Creative Commons license, and indicate if changes were made. The images or other third party material in this stantially more powerful and accessible to projects that critically relied on open article are included in the article’s Creative Commons 16,17— researchers across life and clinical sciences data the jubilees of 2019 remind us license, unless indicated otherwise in a credit line to the – in part because new generations of that bringing mass spectrometry forward material. If material is not included in the article’s Creative Orbitraps and other ESI-based instruments requires both ingenious concepts and public Commons license and your intended use is not permitted have been made commercially available. sharing of the amazing science they spawn. by statutory regulation or exceeds the permitted use, you Operating these instruments has become will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http:// increasingly intuitive and less dependent creativecommons.org/licenses/by/4.0/. on in-depth technical expertise in mass spectrometry. While these technological advances offer exciting opportunities, they © Springer Nature Limited 2019

2 NATURE COMMUNICATIONS | (2019) 10:4029 | https://doi.org/10.1038/s41467-019-12150-4 | www.nature.com/naturecommunications