PXD060333

PXD060333 is an original dataset announced via ProteomeXchange.

Title	QuickProt: a bioinformatics and visualization tool for DIA and PRM mass spectrometry-based proteomics datasets
Description	Mass spectrometry (MS)-based proteomics focuses on identifying and quantifying peptides and proteins in biological samples. Although upstream processing of MS-derived data, including deconvolution, alignment, and peptide-protein prediction, has been achieved through various platforms, the downstream analysis, including quality control, visualizations, and interpretation of proteomics results remain challenging due to the lack of integrated tools to facilitate the analyses. To facilitate downstream interrogation of data-independent acquisition (DIA) and parallel reaction monitoring (PRM) datasets, we developed a series of Python-based Google Colab notebooks called QuickProt. These pipelines were designed so that users with no coding expertise can utilize the tools. Alternatively, as open-source code, users can customize the QuickProt notebooks and incorporate them into their workflows. As proof of concept, we applied QuickProt to analyze in-house DIA and stable isotope dilution (SID)-PRM MS proteomics datasets of a time course of erythropoiesis. The analysis outputs in annotated tables and publication-ready figures revealed a dynamic rearrangement of the proteome during erythroid differentiation, with the abundances of proteins linked to gene regulatory, metabolic, and chromatin remodeling pathways increasing early in the process. Altogether, these tools aim to automate and streamline DIA and PRM-MS proteomics data analysis, making it more efficient and less time-consuming.
HostingRepository	PanoramaPublic
AnnounceDate	2026-06-12
AnnouncementXML	Submission_2026-06-12_15:30:52.748.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Omar Arias-Gaguancela
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-29 11:19:55	ID requested
⏵ 1	2026-06-12 15:30:53	announced

Arias-Gaguancela O, Palii C, Nissa MU, Brand M, Ranish J, QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry-Based Proteomics Datasets. Proteomics, 25(19):62-72(2025) [pubmed]

submitter keyword: QuickProt, QuickProt-DIA, QuickProt-PRM, mass spectrometry (MS), proteomics, data-independent acquisition (DIA), parallel reaction monitoring (PRM), LC-MS/MS, erythropoiesis

Jeff Ranish
contact affiliation	Institute for Systems Biology
contact email	jeff.ranish@isbscience.org
lab head
Omar Arias-Gaguancela
contact affiliation	Institute for Systems Biology
contact email	omar.arias-gaguancela@isbscience.org
dataset submitter

Panorama Public dataset URI