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Spectral Networks: A New Approach to the Identification of Proteins and Post-translational Modifications

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Air date: Friday, September 21, 2007, 10:00:00 AM
Time displayed is Eastern Time, Washington DC Local
Views: Total views: 306 * This only includes stats from October 2011 and forward.
Category: Proteomics
Runtime: 01:16:06
Description: The ongoing success of the proteomics endeavor is the result of a symbiosis between experimental ingenuity and efficient bioinformatics. But despite valuable contributions, the road to a understanding of protein behavior is still hurdled by significant difficulties in the extensive identification of unexpected post-translational modifications and highly modified peptides. Recently, tandem mass spectrometry (MS/MS) based approaches seemed to be reaching the limit on the amount of information that could be extracted from MS/MS spectra. However, a closer look reveals that a common limiting procedure is to analyze each spectrum in isolation,even though high throughput mass spectrometry regularly generates spectra from related peptides.

By capitalizing on this redundancy we show that, similarly to the alignment of protein sequences, unidentified MS/MS spectra can also be aligned for the identification of modified and unmodified variants of the same peptide. Moreover, this alignment procedure can be iterated for the accurate grouping of multiple peptide variants. In fact, when applied to a set of spectra from cataractous lenses proteins from a 93-year old patient, spectral networks were able to capitalize on the highly correlated peaks in spectra from variants of the same peptide to rediscover the modifications identified by database search methods and additionally discovered several novel modification events.

http://proteome.nih.gov
NLM Title: Spectral networks algorithms for de novo interpretation of tandem mass spectra / Nuno Bandeira.
Author: Bandeira, Nuno.
National Institutes of Health (U.S.)
Publisher:
Abstract: (CIT): The ongoing success of the proteomics endeavor is the result of a symbiosis between experimental ingenuity and efficient bioinformatics. But despite valuable contributions, the road to a understanding of protein behavior is still hurdled by significant difficulties in the extensive identification of unexpected post-translational modifications and highly modified peptides. Recently, tandem mass spectrometry (MS/MS) based approaches seemed to be reaching the limit on the amount of information that could be extracted from MS/MS spectra. However, a closer look reveals that a common limiting procedure is to analyze each spectrum in isolation, even though high throughput mass spectrometry regularly generates spectra from related peptides. By capitalizing on this redundancy we show that, similarly to the alignment of protein sequences, unidentified MS/MS spectra can also be aligned for the identification of modified and unmodified variants of the same peptide. Moreover, this alignment procedure can be iterated for the accurate grouping of multiple peptide variants. In fact, when applied to a set of spectra from cataractous lenses proteins from a 93-year old patient, spectral networks were able to capitalize on the highly correlated peaks in spectra from variants of the same peptide to rediscover the modifications identified by database search methods and additionally discovered several novel modification events.
Subjects: Sequence Analysis, Protein
Tandem Mass Spectrometry
Publication Types: Lecture
Webcast
Rights: This is a work of the United States Government.
NLM Classification: QU 450
NLM ID: 101317948
CIT Live ID: 5490
Permanent link: https://videocast.nih.gov/watch=5490

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