PXD002393

PXD002393 is an original dataset announced via ProteomeXchange.

Title	Label-free quantification in ion-mobility enhanced data-independent acquisition proteomics
Description	Data-dependent acquisition (DDA) methods are a well-established tool for proteome analysis and have greatly expedited the field of shotgun proteomics. However, their serial and stochastic nature restricts their reproducibility and limits the detectable dynamic range to the peptides that ionize best. Unbiased data-independent acquisition (DIA) strategies strive to overcome this limitation and have gained increased popularity over recent years. The integration of ion-mobility separation (IMS) into DIA workflows provides an additional dimension of separation and increases the achievable analytical depth of DIA approaches. Here we provide a detailed protocol for a label-free quantitative proteomics workflow based on ion-mobility enhanced DIA, which uses drift time specific collision energies to improve precursor fragmentation efficiency. The protocol comprises a detailed description of all major steps including sample preparation, LC-IMS-MS analysis, and data processing. Our protocol can handle proteome samples of any complexity and enables a highly reproducible and accurate label-free quantitation of up to 5,600 proteins across multiple runs in complete cellular lysates. Depending on the number of samples to be analysed, the protocol takes a minimum of three days to complete from proteolytic digest to data evaluation.
HostingRepository	PRIDE
AnnounceDate	2016-04-07
AnnouncementXML	Submission_2016-04-07_02:35:59.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ute Distler
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse) (Baker's yeast); NCBI TaxID: 643680; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Synapt G2-S HDMS

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-18 05:28:05	ID requested
⏵ 1	2016-04-07 02:36:00	announced

Distler U, Kuharev J, Navarro P, Tenzer S, Label-free quantification in ion mobility-enhanced data-independent acquisition proteomics. Nat Protoc, 11(4):795-812(2016) [pubmed]

curator keyword: Technical

submitter keyword: label-free quantification, ion mobility separation, data-independent acquisition, mass spectrometry, proteomics

Stefan Tenzer
contact affiliation	Institute for Immunology UMC University of Mainz
contact email	tenzer@uni-mainz.de
lab head
Ute Distler
contact affiliation	Universität Mainz
contact email	ute.distler@uni-mainz.de
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/2016/03/PXD002393

PRIDE project URI

• PRIDE
  1. PXD002393
     1. Label: PRIDE project
     2. Name: Label-free quantification in ion-mobility enhanced data-independent acquisition proteomics