Newswise — The editors of the journal Molecular & Cellular Proteomics request feedback from the proteomics community on draft guidelines for publishing proteomics studies that use data-independent acquisition (DIA) methods. The draft guidelines can be accessed at http://www.mcponline.org/site/misc/dia_guidelines_draft.xhtml. Comments will be accepted until the end of September.
“DIA is a rapidly growing research approach that can be employed on a wide variety of instrument platforms,” said Steven Carr, deputy editor of MCP and senior director of proteomics at the Broad Institute. “As such, it is important to establish rules to make sure it is properly applied.”
With technical advances in instrumentation and computation, DIA approaches are growing in popularity, particularly for quantitative studies of sets of related samples. However, because the spectra collected using DIA are significantly more complex than data from other approaches, they can be more difficult to interpret. Complicating the situation further, there are many competing techniques for collecting DIA data, few of which have been compared directly, and fieldwide standards around how to interpret and report results have yet to develop.
Therefore, the journal is taking steps to ensure that future data will be described more systematically. The reporting guidelines, drafted at a satellite meeting after the close of the American Society for Mass Spectrometry’s 2018 meeting, aim to help researchers write a thorough description of how DIA data were collected and interpreted, rendering researchers’ conclusions easier to evaluate.
“When we publish the draft, we will give the opportunity for anyone in the community to send in their comments and suggestions,” said Robert Chalkley of the University of California-San Diego, MCP data management editor.
About data-independent acquisition
Data-independent acquisition (DIA) mass spectrometry is a way of collecting tandem mass spectrometry data. It offers broad coverage of the proteome with high run-to-run reproducibility.
In mass spectrometry, for reliable identification of a molecule, you need to know its intact precursor ion mass and also the masses produced when it is fragmented. Most strategies involve fragmenting a single precursor ion at a time. Selection of a precursor ion can be based on observation of a component (a strategy known as data-dependent acquisition (DDA)), or it can be from a list of pre-determined components of interest; i.e. targeted analysis. However, both of these approaches only select a subset of the components present for fragmentation analysis. In DIA acquisition, the whole mass range is fragmented over a series of scans, ensuring fragmentation information about all components is acquired, although at the expense of generally fragmenting multiple components at the same time.
About the drafting process
The journal Molecular & Cellular Proteomics (MCP) hosted a workshop on June 8 to formalize publication guidelines for nontargeted data-independent acquisition and analysis of mass spectra.
The workshop took place in San Diego after the close of the 66th American Society for Mass Spectrometry Conference. It was organized by Carr, Chalkley, and Saddiq Zahari, MCP editor for manuscript integrity.
Among the 24 experts who attended were leading academic experts in DIA, representatives from manufacturers of instruments, and several specialist software packages used for DIA analysis. In addition to MCP, other sponsors of the workshop included the Waters Corp., Bruker and Thermofisher Scientific.
About Molecular & Cellular Proteomics
Molecular & Cellular Proteomics showcases research into proteomes, large-scale sets of proteins from different organisms or biological contexts. The journal publishes work that describes the structural and functional properties of proteins and their expression, particularly with respect to developmental time courses. As part of that mission, MCP has led the field in producing guidelines that aim to allow independent assessment of the reliability of published datasets. For more information about MCP, visit www.mcponline.org.
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