PXD013477

PXD013477 is an original dataset announced via ProteomeXchange.

Title	Assessing the relationship between mass window width and retention time scheduling on protein coverage for data-independent acquisition
Description	Due to the technical advances of mass spectrometers especially the high scanning speed and high MS/MS resolution, the data independent acquisition mass spectrometry (DIA-MS) began to be widely used, which enables high reproducibility in both proteomic identification and quantification. The current DIA-MS methods normally cover a wide mass range, with the aim to target and identify as many peptides and proteins as possible and therefore regularly generates MS/MS spectra of high complexity. In this report, we assessed the performance and benefits of using small windows with e.g. 5-Da width across the peptide elution time. We also devised a new DIA method named RTwinDIA that schedules the small isolation windows in different retention time blocks. We applied Maxquant and pFind database searching tools, and further used Spectronaut with an external comprehensive spectral library of human proteins to perform the direct proteomic identification. We conclude that softwares like pFind have potential in directly analyzing DIA data acquired with small windows, and that the instrumental time and DIA cycle time should be preferably spend on small windows rather than on covering a broad mass range by large windows, to improve the proteome coverage for new biological samples and to increase the quantitative precision. These results further provide perspectives for the future emerge between DDA and DIA on faster MS analyzers.
HostingRepository	PRIDE
AnnounceDate	2019-07-01
AnnouncementXML	Submission_2019-07-01_00:56:18.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yansheng Liu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2019-04-12 02:30:56	ID requested
⏵ 1	2019-07-01 00:56:19	announced

Li W, Chi H, Salovska B, Wu C, Sun L, Rosenberger G, Liu Y, Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition. J Am Soc Mass Spectrom, 30(8):1396-1405(2019) [pubmed]

submitter keyword: DIA-MS, Oribtrap Fusion Lumos, Window size, Scheduling, RTwinDIA

Yansheng Liu
contact affiliation	Department of Pharmacology Cancer Biology Institute Yale University School of Medicine
contact email	yansheng.liu@yale.edu
lab head
Yansheng Liu
contact affiliation	Yale University School of Medicine
contact email	yansheng.liu@yale.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD013477
     1. Label: PRIDE project
     2. Name: Assessing the relationship between mass window width and retention time scheduling on protein coverage for data-independent acquisition