PXD030431-1

PXD030431 is an original dataset announced via ProteomeXchange.

Title	Improving peptide fragment ion detection using travelling wave ion mobility spectrometry with signal enhancement MSE (seMSE)
Description	Recently, a solution to inherent poor ion beam sampling of time-of-flight (TOF) mass analyzers was proposed by restricting detection to ions expected at specific arrival times after being separated in a travelling wave ion mobility spectrometry (TWIMS) cell. Here, we show that this approach can be applied to data independent acquisition (DIA) using a so-called signal enhancement MSE (seMSE) experiment, which was compared to two different TWIMS-DDA and three different TWIMS-MSE methods with respect to the number of peptide identifications, the spectral quality of supporting peptide spec-tra matches, and, more importantly, fragment ion sensitivity. Comparison of fragment ion summed areas showed that seM-SE showed 6.8 to 11.5-fold improvement in fragment ion detection when compared to other MSE methods and although co-fragmentation of co-eluting peptides limited the seMSE peptide identifications it was possible to consistently detect peptides of interest by integrating DDA and MSE results within Skyline.
HostingRepository	PanoramaPublic
AnnounceDate	2022-08-01
AnnouncementXML	Submission_2022-08-01_09:37:06.289.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Juan Camilo Rojas Echeverri
SpeciesList	scientific name: Oryctolagus cuniculus; NCBI TaxID: 9986; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Bos taurus; NCBI TaxID: 9913; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	Dehydrated; Carbamyl; Methyl; Carboxymethyl; Oxidation; Glu->pyro-Glu; Biotin-PEO-Amine; Carbamidomethyl; Deamidated; Acetyl; Gln->pyro-Glu; Pro->Pyrrolidinone; DAET; Propionamide; Ammonia-loss; Dethiomethyl; Cation:Na
Instrument	SYNAPT G2-Si

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-15 18:24:49	ID requested
⏵ 1	2022-08-01 09:37:07	announced

Rojas Echeverri JC, Volke D, Milkovska-Stamenova S, Hoffmann R, ). Anal Chem, 94(31):10930-10941(2022) [pubmed]

submitter keyword: DDA, DIA, MSE, travelling wave ion mobility spectrometry (TWIMS), LC-TWIMS-MS/MS

Ralf Hoffmann
contact affiliation	Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig; Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
contact email	ralf.hoffmann@bbz.uni-leipzig.de
lab head
Juan Camilo Rojas Echeverri
contact affiliation	Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig; Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
contact email	juan_camilo.rojas_echeverri@uni-leipzig.de
dataset submitter

Panorama Public dataset URI