PXD001592

PXD001592 is an original dataset announced via ProteomeXchange.

Title	The impact II, a very high resolution quadrupole time-of-flight instrument for deep shotgun proteomics
Description	Hybrid quadrupole time-of-flight (QTOF) is one of the two major mass spectrometric technologies used in proteomics. Although based on simple fundamental principles, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated LC system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high MS/MS frequencies. The new reflectron and detector improve resolving power compared to the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4,800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2>0.99) and accurate fold change determination in spike-in experiments over three orders of magnitude in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originated from different tissues. Finally, after high pH reversed-phase fractionation we identified 9,515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in cerebellum – the highest proteome coverage measured with a QTOF instrument so far.
HostingRepository	PRIDE
AnnounceDate	2015-05-26
AnnouncementXML	Submission_2015-05-26_05:27:26.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Bruker Daltonics instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2014-12-10 01:38:15	ID requested
⏵ 1	2015-05-26 05:27:27	announced

Beck S, Michalski A, Raether O, Lubeck M, Kaspar S, Goedecke N, Baessmann C, Hornburg D, Meier F, Paron I, Kulak NA, Cox J, Mann M, The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics. Mol Cell Proteomics, 14(7):2014-29(2015) [pubmed]

curator keyword: Technical

submitter keyword: QTOF, Proteomics, LC_MS/MS

Matthias Mann
contact affiliation	Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.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/2015/05/PXD001592

PRIDE project URI

• PRIDE
  1. PXD001592
     1. Label: PRIDE project
     2. Name: The impact II, a very high resolution quadrupole time-of-flight instrument for deep shotgun proteomics