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 Mass spectrometry sheds new light on thallium poisoning cold case
14.12.2018 | University of Maryland

nachricht Protein involved in nematode stress response identified
14.12.2018 | University of Illinois College of Agricultural, Consumer and Environmental Sciences

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Data use draining your battery? Tiny device to speed up memory while also saving power

The more objects we make "smart," from watches to entire buildings, the greater the need for these devices to store and retrieve massive amounts of data quickly without consuming too much power.

Millions of new memory cells could be part of a computer chip and provide that speed and energy savings, thanks to the discovery of a previously unobserved...

Im Focus: An energy-efficient way to stay warm: Sew high-tech heating patches to your clothes

Personal patches could reduce energy waste in buildings, Rutgers-led study says

What if, instead of turning up the thermostat, you could warm up with high-tech, flexible patches sewn into your clothes - while significantly reducing your...

Im Focus: Lethal combination: Drug cocktail turns off the juice to cancer cells

A widely used diabetes medication combined with an antihypertensive drug specifically inhibits tumor growth – this was discovered by researchers from the University of Basel’s Biozentrum two years ago. In a follow-up study, recently published in “Cell Reports”, the scientists report that this drug cocktail induces cancer cell death by switching off their energy supply.

The widely used anti-diabetes drug metformin not only reduces blood sugar but also has an anti-cancer effect. However, the metformin dose commonly used in the...

Im Focus: New Foldable Drone Flies through Narrow Holes in Rescue Missions

A research team from the University of Zurich has developed a new drone that can retract its propeller arms in flight and make itself small to fit through narrow gaps and holes. This is particularly useful when searching for victims of natural disasters.

Inspecting a damaged building after an earthquake or during a fire is exactly the kind of job that human rescuers would like drones to do for them. A flying...

Im Focus: Topological material switched off and on for the first time

Key advance for future topological transistors

Over the last decade, there has been much excitement about the discovery, recognised by the Nobel Prize in Physics only two years ago, that there are two types...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

ICTM Conference 2019: Digitization emerges as an engineering trend for turbomachinery construction

12.12.2018 | Event News

New Plastics Economy Investor Forum - Meeting Point for Innovations

10.12.2018 | Event News

EGU 2019 meeting: Media registration now open

06.12.2018 | Event News

 
Latest News

Data use draining your battery? Tiny device to speed up memory while also saving power

14.12.2018 | Power and Electrical Engineering

Tangled magnetic fields power cosmic particle accelerators

14.12.2018 | Physics and Astronomy

In search of missing worlds, Hubble finds a fast evaporating exoplanet

14.12.2018 | Physics and Astronomy

VideoLinks
Science & Research
Overview of more VideoLinks >>>