PXD063416

PXD063416 is an original dataset announced via ProteomeXchange.

Title	Decoding the impact of isolation window selection and QuantUMS filtering in DIA-NN for DIA quantification of peptides and proteins.
Description	Proteomic studies using Data Independent Acquisition (DIA) have gained momentum in all fields of biology. Search engines are evolving to keep up with the latest developments in instrument technology. DIA-NN is the most popular software for DIA analysis under academic use license. The QuantUMS algorithm in DIA-NN improves quantification quality control by calculating three scores (Protein Group MaxLFQ Quality, Empirical Quality, and Quantity Quality) that assess the agreement between MS1 ​​and MS2 features. Here, we show that applying specific cutoffs to these scores can significantly impact results. To enable you to make a more informed decision about what represents a reasonable tradeoff (identification and quantification), we evaluated the impact of different combinations of the scores on data acquired using different isolation windows using a mixture of two-species with known ratio. We compared six different versions of DIA-NN and found high reproducibility across versions, except for version 1.9. We show that filtering by QuantUMS scores removes proteins with low abundance and high coefficients of variation. Finally, we develop the QC4DIANN Shiny application in R language for interactive quality control automation.
HostingRepository	PRIDE
AnnounceDate	2025-12-04
AnnouncementXML	Submission_2025-12-04_13:06:35.384.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alison Chaves
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-28 22:35:42	ID requested
⏵ 1	2025-12-04 13:06:35	announced

10.1021/ACS.JPROTEOME.5C00009;

submitter keyword: isolation window, DIA, mass spectrometry,QuantUMS, quantification

Solange Maria de Toledo Serrano
contact affiliation	Laboratory of applied toxinology Center of Toxins, Immune-Response and Cell Signaling (CeTICS) Butantan Institute
contact email	solange.serrano@butantan.gov.br
lab head
Alison Chaves
contact affiliation	Butantan Institute
contact email	felipealison@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063416
     1. Label: PRIDE project
     2. Name: Decoding the impact of isolation window selection and QuantUMS filtering in DIA-NN for DIA quantification of peptides and proteins.