PXD009861

PXD009861 is an original dataset announced via ProteomeXchange.

Title	Fast open modification spectral library searching through approximate nearest neighbor indexing
Description	Open modification searching (OMS) is a powerful search strategy that identifies peptides carrying any type of modification by allowing a modified spectrum to match against its unmodified variant by using a very wide precursor mass window. A drawback of this strategy, however, is that it leads to a large increase in search time. Although performing an open search can be done using existing spectral library search engines by simply setting a wide precursor mass window, none of these tools have been optimized for OMS, leading to excessive runtimes and suboptimal identification results. This data set contains the evaluation results of the ANN-SoLo tool for fast and accurate open spectral library searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up OMS by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This approach is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate, as well as a shifted dot product score to sensitively match modified spectra to their unmodified counterparts. ANN-SoLo achieves state-of-the-art performance in terms of speed and the number of identifications. On a previously published human cell line data set, ANN-SoLo confidently identifies more spectra than SpectraST or MSFragger and achieves a speedup of an order of magnitude compared to SpectraST.
HostingRepository	PRIDE
AnnounceDate	2018-09-25
AnnouncementXML	Submission_2018-09-28_08:45:42.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wout Bittremieux
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-22 08:57:04	ID requested
1	2018-09-25 08:57:35	announced
⏵ 2	2018-09-28 08:45:44	announced	Updated publication reference for PubMed record(s): 30184435.

Bittremieux W, Meysman P, Noble WS, Laukens K, Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing. J Proteome Res, 17(10):3463-3474(2018) [pubmed]

curator keyword: Technical

submitter keyword: open modification searching, spectral library, PTM

Kris Laukens
contact affiliation	Department of Mathematics and Computer Science, University of Antwerp, Belgium
contact email	kris.laukens@uantwerpen.be
lab head
Wout Bittremieux
contact affiliation	University of Antwerp
contact email	wout.bittremieux@uantwerpen.be
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/09/PXD009861

PRIDE project URI

• PRIDE
  1. PXD009861
     1. Label: PRIDE project
     2. Name: Fast open modification spectral library searching through approximate nearest neighbor indexing