PXD009861 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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_2018-09-25_08:57:34.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 |
Dataset History
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. |
Publication List
Dataset with its publication pending |
Keyword List
curator keyword: Technical |
submitter keyword: open modification searching, spectral library, PTM |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD009861
- Label: PRIDE project
- Name: Fast open modification spectral library searching through approximate nearest neighbor indexing