PXD003317

PXD003317 is an original dataset announced via ProteomeXchange.

Title	Application of de novo sequencing to large-scale complex proteomics datasets
Description	Dependent on concise, pre-defined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference databases. However, such algorithms have been difficult to apply to complex protein mixtures, in part due to a lack of methods for automatically validating de novo sequencing results. Here, we present novel metrics for benchmarking de novo sequencing algorithm performance on large scale proteomics datasets, and present a method for accurately calibrating false discovery rates on de novo results. We also present a novel algorithm (LADS) which leverages experimentally disambiguated fragmentation spectra to boost sequencing accuracy and sensitivity. LADS improves sequencing accuracy on longer peptides relative to other algorithms and improves discriminability of correct and incorrect sequences. Using these advancements, we demonstrate accurate de novo identification of peptide sequences not identifiable using database search-based approaches.
HostingRepository	PRIDE
AnnounceDate	2016-01-12
AnnouncementXML	Submission_2016-01-12_06:54:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Arun Devabhaktuni
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-12-10 01:09:38	ID requested
⏵ 1	2016-01-12 06:54:16	announced

Devabhaktuni A, Elias JE, Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets. J Proteome Res, 15(3):732-42(2016) [pubmed]

curator keyword: Technical

submitter keyword: mass spectrometry, de novo peptide sequencing, MS/MS, Proteomics, large-scale computational analysis, yeast, bos

Joshua E. Elias
contact affiliation	Stanford University Department of Chemical and Systems Biology
contact email	jee3@stanford.edu
lab head
Arun Devabhaktuni
contact affiliation	Stanford University Chemical and Systems Biology
contact email	arund@stanford.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD003317
     1. Label: PRIDE project
     2. Name: Application of de novo sequencing to large-scale complex proteomics datasets