PXD017823

PXD017823 is an original dataset announced via ProteomeXchange.

Title	Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics.
Description	Multiplexed quantitative analyses of complex proteomes enable deep biological insight. While a multitude of workflows have been developed for multiplexed analyses, the most quantitatively accurate method (SPS-MS3) suffers from long acquisition duty cycles. We built a new, real-time database search (RTS) platform, Orbiter, to combat the SPS-MS3 method’s longer duty cycles. RTS with Orbiter eliminates SPS-MS3 scans if no peptide matches to a given spectrum. With Orbiter’s online proteomic analytical pipeline, which includes RTS and false discovery rate analysis, it was possible to process a single spectrum database search in less than 10 milliseconds. The result is a fast, functional means to identify peptide spectral matches using Comet, filter these matches, and more efficiently quantify proteins of interest. Importantly, the use of Comet for peptide spectral matching allowed for a fully featured search, including analysis of post-translational modifications, with well-known and extensively validated scoring. These data could then be used to trigger subsequent scans in an adaptive and flexible manner. In this work we tested the utility of this adaptive data acquisition platform to improve the efficiency and accuracy of multiplexed quantitative experiments. We found that RTS enabled a two-fold increase in mass spectrometric data acquisition efficiency. Orbiter’s RTS quantified more than 8000 proteins across 10 proteomes in half the time of an SPS-MS3 analysis (18 hours for RTS, 36 hours for SPS-MS3).
HostingRepository	PRIDE
AnnounceDate	2020-04-09
AnnouncementXML	Submission_2020-04-09_01:31:34.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Devin Schweppe
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-02 02:48:08	ID requested
⏵ 1	2020-04-09 01:32:04	announced

Schweppe DK, Eng JK, Yu Q, Bailey D, Rad R, Navarrete-Perea J, Huttlin EL, Erickson BK, Paulo JA, Gygi SP, Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics. J Proteome Res, 19(5):2026-2034(2020) [pubmed]

submitter keyword: multiplexed, real-time search, Orbiter

Steven Gygi
contact affiliation	Professor, Harvard Medical School
contact email	steven_gygi@hms.harvard.edu
lab head
Devin Schweppe
contact affiliation	Harvard Medical School
contact email	devin_schweppe@hms.harvard.edu
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/2020/04/PXD017823

PRIDE project URI

• PRIDE
  1. PXD017823
     1. Label: PRIDE project
     2. Name: Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics.