PXD018445

PXD018445 is an original dataset announced via ProteomeXchange.

Title	Using instrument logic to improve identifications in low stoichiometry SILAC/TMT experiments
Description	Pulsed SILAC approaches allow measurement of protein dynamics, including protein translation and degradation. However, its use in quantifying acute changes has been limited due the low labeled peptide stoichiometry. Here, we describe the use of instrument logic to select peaks of interest via targeted mass differences (TMD) for overcoming this limitation. Comparing peptides artificially mixed at low heavy-to-light stoichiometry measured using standard data dependent acquisition with or without TMD revealed 2-3 fold increases in identification without significant loss in quantification precision for both MS2 and MS3 methods. Our benchmarked method approach increases throughput by reducing the necessary machine time. We anticipate that all pulsed SILAC measurements, if combined with TMT or not, would greatly benefit from instrument logic based approaches.
HostingRepository	PRIDE
AnnounceDate	2020-05-29
AnnouncementXML	Submission_2020-05-29_01:38:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kevin Klann
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; isotope labeled residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-09 04:20:04	ID requested
⏵ 1	2020-05-29 01:38:15	announced

Klann K, M, ü, nch C, Instrument Logic Increases Identifications during Mutliplexed Translatome Measurements. Anal Chem, 92(12):8041-8045(2020) [pubmed]

submitter keyword: TMT, SILAC, Protein dynamics,

Christian Münch
contact affiliation	Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany Frankfurt Cancer Institute, Frankfurt am Main, Germany Cardio-Pulmonary Institute, Frankfurt am Main, Germany
contact email	ch.muench@em.uni-frankfurt.de
lab head
Kevin Klann
contact affiliation	Universitätsklinikum Frankfurt am Main
contact email	klann@em.uni-frankfurt.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/2020/05/PXD018445

PRIDE project URI

• PRIDE
  1. PXD018445
     1. Label: PRIDE project
     2. Name: Using instrument logic to improve identifications in low stoichiometry SILAC/TMT experiments