PXD044292-1

PXD044292 is an original dataset announced via ProteomeXchange.

Title	Full Mass Range PhiSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis
Description	Optimizing data-independent acquisition (DIA) methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here we describe the full mass range application of Phase-constrained Spectrum Deconvolution Method (PhiSDM) for OrbitrapTM mass spectrometry in real time, and compare its performance to the standard enhanced Fourier transformation (eFT). We show that the increased resolving power of PhiSDM is beneficial in areas of high spectral complexity and comes with a greater ability to resolve low-abundance signals. In a 2-hour analysis of 200 ng HeLa digest, this resulted in an increase of 8% and 16% in the number of quantified protein groups and peptides, respectively. As the acquisition speed becomes even more important when using short chromatographic gradients, we further applied PhiSDM methods to a range of shorter gradient lengths (21, 12, and 5 min). While PhiSDM improved identification rates and spectral quality in all tested gradients, it proved particularly advantageous for the 5 min gradient. Here the number of protein groups and peptides identified increased by >15% in comparison to eFT processing. In conclusion, PhiSDM is an alternative signal processing algorithm for processing FTMS data that can increase spectral quality and provide quantification benefits for LC-MS acquisitions especially when using short gradient.
HostingRepository	PRIDE
AnnounceDate	2024-01-09
AnnouncementXML	Submission_2024-01-09_06:16:21.164.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;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-02 02:09:47	ID requested
⏵ 1	2024-01-09 06:16:21	announced
2	2024-10-22 06:19:53	announced	2024-10-22: Updated project metadata.

10.1016/J.MCPRO.2024.100713;

submitter keyword: proteomics,Orbitrap, high-throughput, data-independent acquisition, PhiSDM

Matthias Mann
contact affiliation	Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany NNF Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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. PXD044292
     1. Label: PRIDE project
     2. Name: Full Mass Range PhiSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis