PXD037766

PXD037766 is an original dataset announced via ProteomeXchange.

Title	Synchro-PASEF slices peptide precursors enabling specific fragment extraction and interference removal in data independent acquisition
Description	Data independent acquisition methods have become increasingly popular in mass spectrometry (MS)-based proteomics because they enable parallel and continuous acquisition of fragment spectra. However, these advantages come with the challenge of correctly reconstructing the precursor-fragment relationship in these highly multiplexed spectra for reliable identification and quantification. Here we introduce a scan mode for the combination of trapped ion mobility spectrometry (TIMS) with parallel accumulation – serial fragmentation (PASEF) that naturally and continuously follows the ion cloud in ion mobility and peptide mass dimensions as opposed to the step functions we employed before. Termed synchro-PASEF, it increases fragment yield several fold at sub-second cycle times. The quadrupole selection window moves synchronously through the mass and ion mobility range, deconvoluting the DIA spectra and defining precursor-quadrupole relationships. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor – fragment relationship in ion mobility and mass dimensions. Importantly, the two parts of the fragment ion transitions in synchro-PASEF provide a further dimension of specificity via a lock and key mechanism. This is especially advantageous for quantification, where signals from interfering precursors in the dia selection window only affect the top or bottom part of the fragment ion, allowing them to be filtered out. In this paper, we establish the defining features of synchro-PASEF and explore its potential for proteomics analyses.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:51:36.396.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Oryctolagus cuniculus (Rabbit); NCBI TaxID: 9986; scientific name: Candida albicans (Yeast); NCBI TaxID: 5476; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-27 02:50:12	ID requested
1	2023-03-10 13:01:26	announced
⏵ 2	2023-11-14 07:51:39	announced	2023-11-14: Updated project metadata.

Skowronek P, Krohs F, Lubeck M, Wallmann G, Itang ECM, Koval P, Wahle M, Thielert M, Meier F, Willems S, Raether O, Mann M, Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition. Mol Cell Proteomics, 22(2):100489(2023) [pubmed]

submitter keyword: PASEF, TOF, rapid analysis,TIMS, data-independent acquisition, scan mode

Matthias Mann
contact affiliation	Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD037766
     1. Label: PRIDE project
     2. Name: Synchro-PASEF slices peptide precursors enabling specific fragment extraction and interference removal in data independent acquisition