PXD051331

PXD051331 is an original dataset announced via ProteomeXchange.

Title	MGVB: a new proteomics toolset for fast and efficient data analysis
Description	MGVB is a collection of tools for proteomics data analysis. It covers data processing from in silico digestion of protein sequences to comprehensive identification of postranslational modifications and solving the protein inference problem. The toolset is developed with efficiency in mind. It enables analysis at a fraction of the resources cost typically required by existing commercial and free tools. MGVB, as it is a native application, is much faster than existing proteomics tools such as MaxQuant and MSFragger and, in the same time, finds very similar, in some cases even larger number of peptides at a chosen level of statistical significance. It implements a probabilistic scoring function to match spectra to sequences, and a novel combinatorial search strategy for finding post-translational modifications, and a Bayesian approach to locate modification sites. This report describes the algorithms behind the tools, presents benchmarking data sets analysis comparing MGVB performance to MaxQuant/Andromeda, and provides step by step instructions for using it in typical analytical scenarios. The toolset is provided free to download and use for academic research and in software projects, but is not open source at the present. It is the intention of the author that it will be made open source in the near future—following rigorous evaluations and feedback from the proteomics research community.
HostingRepository	PRIDE
AnnounceDate	2024-11-15
AnnouncementXML	Submission_2024-11-15_00:35:25.662.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Metodi Metodiev
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-10 05:26:10	ID requested
⏵ 1	2024-11-15 00:35:26	announced

10.1016/J.EBIOM.2016.05.009;

10.1016/j.ebiom.2016.05.009;

Metodieva G, Adoki S, Lausen B, Metodiev MV, Decreased Usage of Specific Scrib Exons Defines a More Malignant Phenotype of Breast Cancer With Worsened Survival. EBioMedicine, 8():150-158(2016) [pubmed]

submitter keyword: post-translational modifications, mass spectrometry, MS/MS search engine,software for computational proteomics, shotgun analysis

Metodi V.
contact affiliation	University of Essex, UK
contact email	mmetod@essex.ac.uk
lab head
Metodi Metodiev
contact affiliation	University of Essex
contact email	mmetod@essex.ac.uk
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/2024/11/PXD051331

PRIDE project URI

• PRIDE
  1. PXD051331
     1. Label: PRIDE project
     2. Name: MGVB: a new proteomics toolset for fast and efficient data analysis