Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Unidentified spectra detector

28.06.2016

Detecting millions of consistently unidentified spectra in vast tracts of proteomics data is possible with a new algorithm developed at EMBL-EBI

A new algorithm clusters the millions of peptide mass spectra in the PRIDE Archive public database, making it easier to detect millions of consistently unidentified spectra across different datasets. Published in Nature Methods, the new tool is an important step towards fully exploiting data produced in discovery proteomics experiments.


"Creating a sensible subset of spectra to start an in-depth analysis of unidentified spectra has been very challenging," says Juan Antonio Vizcaino of EMBL-EBI.

Credit: Illustration by Spencer Phillips, EMBL-EBI

On average, almost three quarters of spectra measured in discovery proteomics experiments remain unidentified, regardless of the quality of the experiment, as they cannot be interpreted by standard sequence-based search engines.

Alternative approaches to improve the rate of identification exist, but are fraught with disadvantages including ambiguous results. In today's study, researchers working on the PRIDE Archive public repository of proteomics data present a large-scale 'spectrum clustering' solution that takes advantage of the growing number of mass spectrometry (MS) datasets to systematically study millions of unidentified spectra.

"MS experiments produce huge amounts of data, but identifying meaningful sequences that could be assigned to specific biological functions can be troublesome," says Johannes Griss, formerly at EMBL-EBI in the UK and now at the Medical University of Vienna, Austria.

"Discovery proteomics is a mature technology, and it's crucial that we are able to exploit the data efficiently."

One of the challenges with these technologies is that a large proportion of the data generated can't be interpreted, as they correspond to peptides that have not yet been observed and are not available in databases. Such spectra could correspond to peptide variants derived from individual generic variation, or to peptides containing post-translational modifications, which are essential for the biological functions of proteins.

"What we have now is an algorithm that shows us patterns, or groups of spectra, that we've consistently missed, and helps us figure out which ones are good enough to pursue," adds Johannes. "It's a valuable tool that helps us unpick what's going on in proteomics, so we can better understand basic biological processes."

The team used the approach to recognise 9 million consistently unidentified spectra, which can make post-translational modifications and peptides containing sequence variants more discoverable. They identified three distinct sets of spectra: those that have been incorrectly identified, those that are not of high enough quality to identify properly, and those that are truly unidentified. They also combined their new approach with other methods to identify roughly 20% of the originally unidentified spectra in the public archive.

"Discovery proteomics is a mature technology, and it's crucial that we are able to exploit the data efficiently - but creating a sensible subset of spectra to start an in-depth analysis of unidentified spectra has been very challenging," says Juan Antonio Vizcaíno, who leads the Proteomics team at EMBL-EBI. "We developed a comparatively lightweight computational approach that makes it much easier to detect sequences that have been incorrectly identified, or consistently observed but not identified. These ready-to-use collections of commonly unidentified spectra are a resource for the community, so that we can all pool our efforts to find lasting solutions for proteomics research."

The new algorithm will be used to improve quality control in the PRIDE Archive. The complete spectrum clustering results are available through the PRIDE Cluster resource, which aims to simplify further investigation into unidentified spectra.

###

Source article: Griss J., et al. (2016). Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. Nature Methods (in press). DOI: 10.1038/nmeth.3902

Media Contact

Mary Todd Bergman
mary@ebi.ac.uk
44-788-137-7941

http://www.ebi.ac.uk 

Mary Todd Bergman | EurekAlert!

More articles from Life Sciences:

nachricht NYSCF researchers develop novel bioengineering technique for personalized bone grafts
18.07.2018 | New York Stem Cell Foundation

nachricht Pollen taxi for bacteria
18.07.2018 | Technische Universität München

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: First evidence on the source of extragalactic particles

For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.

To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...

Im Focus: Magnetic vortices: Two independent magnetic skyrmion phases discovered in a single material

For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.

Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...

Im Focus: Breaking the bond: To take part or not?

Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.

A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...

Im Focus: New 2D Spectroscopy Methods

Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.

"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....

Im Focus: Chemical reactions in the light of ultrashort X-ray pulses from free-electron lasers

Ultra-short, high-intensity X-ray flashes open the door to the foundations of chemical reactions. Free-electron lasers generate these kinds of pulses, but there is a catch: the pulses vary in duration and energy. An international research team has now presented a solution: Using a ring of 16 detectors and a circularly polarized laser beam, they can determine both factors with attosecond accuracy.

Free-electron lasers (FELs) generate extremely short and intense X-ray flashes. Researchers can use these flashes to resolve structures with diameters on the...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Leading experts in Diabetes, Metabolism and Biomedical Engineering discuss Precision Medicine

13.07.2018 | Event News

Conference on Laser Polishing – LaP: Fine Tuning for Surfaces

12.07.2018 | Event News

11th European Wood-based Panel Symposium 2018: Meeting point for the wood-based materials industry

03.07.2018 | Event News

 
Latest News

NYSCF researchers develop novel bioengineering technique for personalized bone grafts

18.07.2018 | Life Sciences

Machine-learning predicted a superhard and high-energy-density tungsten nitride

18.07.2018 | Materials Sciences

Why might reading make myopic?

18.07.2018 | Health and Medicine

VideoLinks
Science & Research
Overview of more VideoLinks >>>