PXD022778 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant |
Description | The standard proteomics database search strategy involves searching spectra against a peptide database and estimating the false discovery rate (FDR) of the resulting set of peptide-spectrum matches. One assumption of this protocol is that all the peptides in the database are reDR control strategies are needed. Recently, two methods were proposed to address this problem: subset-search and all-sub. We show that both methods fail to control the FDR. For subset-search, this failure is due to the presence of “neighbor” peptides, which are defined as irrelevant peptides with a similar precursor mass and fragmentation spectrum as a relevant peptide. Not considering neighbors compromises the FDR estimate because a spectrum generated by an irrelevant peptide can incorrectly match well to a relevant peptide. Therefore, we have developed a new method, “filter then subset-neighbor search” (FSNS), that accounts for neighbor peptides. We show evidence that FSNS properly controls the FDR when neighbors are present and that FSNS outperforms group-FDR, the only other method able to control the FDR relative to a subset of relevant peptides |
HostingRepository | PRIDE |
AnnounceDate | 2021-07-12 |
AnnouncementXML | Submission_2021-07-11_21:51:33.182.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Andy Lin |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; scientific name: Ricinus communis; NCBI TaxID: 3988; |
ModificationList | iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos; Q Exactive HF; LTQ Orbitrap Velos; Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-11-26 22:52:51 | ID requested | |
1 | 2021-06-18 03:55:24 | announced | |
⏵ 2 | 2021-07-11 21:51:33 | announced | 2021-07-12: Updated project metadata. |
Publication List
Lin A, Plubell DL, Keich U, Noble WS, Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant. J Proteome Res, 20(8):4153-4164(2021) [pubmed] |
Keyword List
submitter keyword: UPS1, ricin, yeast, castor,human |
Contact List
Willian Stafford Noble |
contact affiliation | University of Washington |
contact email | william-noble@uw.edu |
lab head | |
Andy Lin |
contact affiliation | University of Washington |
contact email | linandy@uw.edu |
dataset submitter | |
Full Dataset Link List
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/2021/06/PXD022778 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD022778
- Label: PRIDE project
- Name: Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant