PXD005280

PXD005280 is an original dataset announced via ProteomeXchange.

Title	Combining de novo peptide sequencing algorithms, a synergistic approach to boost both identifications and confidence in bottom-up proteomics
Description	Complex MS-based proteomics datasets are usually analyzed by protein database-searches. While this approach performs considerably well for sequenced organisms, direct inference of peptide sequences from tandem mass spectra, i.e. de novo peptide sequencing, oftentimes is the only way to obtain information when protein databases are absent. However, available algorithms suffer from drawbacks such as lack of validation and often high rates of false positive hits (FP). Here we present a simple method of combining results from commonly available de novo peptide sequencing algorithms, which in conjunction with minor tweaks in data acquisition ensues lower empirical FDR compared to the analysis using single algorithms. Results were validated using state-of-the art database search algorithms as well specifically synthesized reference peptides. Thus, we could increase the number of PSMs meeting a stringent FDR of 5% more than threefold compared to the single best de novo sequencing algorithm alone, accounting for an average of 11,120 PSMs (combined) instead of 3,476 PSMs (alone) in triplicate 2 h LC-MS runs of tryptic HeLa digestion.
HostingRepository	PRIDE
AnnounceDate	2019-09-25
AnnouncementXML	Submission_2019-09-25_04:22:24.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bernhard Blank-Landeshammer
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Radix auricularia; NCBI TaxID: 52793; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-07 01:40:16	ID requested
⏵ 1	2019-09-25 04:22:25	announced

Blank-Landeshammer B, Kollipara L, Bi, ß K, Pfenninger M, Malchow S, Shuvaev K, Zahedi RP, Sickmann A, Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics. J Proteome Res, 16(9):3209-3218(2017) [pubmed]

curator keyword: Technical

submitter keyword: De novo peptide sequencing, bottom-up proteomics, LC-MS/MS, false discovery rate

Prof. Dr. Albert Sickmann
contact affiliation	Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Germany
contact email	sickmann@isas.de
lab head
Bernhard Blank-Landeshammer
contact affiliation	Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund
contact email	bernhard.blank@isas.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005280
     1. Label: PRIDE project
     2. Name: Combining de novo peptide sequencing algorithms, a synergistic approach to boost both identifications and confidence in bottom-up proteomics