Article Synopsis
- MaxDIA is a software platform designed for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant environment, achieving enhanced proteome coverage and improved protein quantification accuracy.
- It utilizes spectral libraries and machine learning to provide accurate false discovery rate (FDR) estimates and enables hypothesis-free analysis of DIA samples, ensuring reliable results even without a library.
- MaxDIA's advanced features include three- or four-dimensional fragment data detection and a unique bootstrap workflow for enhanced data accuracy, especially when combined with new technologies like BoxCar acquisition and trapped ion mobility spectrometry.
Video Abstracts
Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA-hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA's bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies-BoxCar acquisition and trapped ion mobility spectrometry-both lead to deep and accurate proteome quantification.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8668435 | PMC |
| http://dx.doi.org/10.1038/s41587-021-00968-7 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Longitudinal Autoantibody and Proteomic Profiles Uncover Biomarkers and Mechanisms of Disease Progression in Systemic Sclerosis.
Arthritis Rheumatol
August 2025
Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
Objective: To evaluate dynamic changes in autoantibody and proteomic profiles in treatment-naïve systemic sclerosis (SSc) patients and identify biomarkers and mechanisms associated with disease progression.
Methods: Serum samples from 30 baseline and 49 follow-up SSc patients, along with 38 controls, were analyzed. Autoantibody profiles were assessed using an autoantigen microarray targeting 120 autoantibodies, while proteomic analysis was conducted via liquid chromatography-mass spectrometry in data-independent acquisition mode.
Apoptosis regulates intestinal regeneration via iPLA2 and EGFL7 signaling in .
Zool Res
September 2025
State Key Laboratory of Agricultural Products Safety, Ningbo University, Ningbo, Zhejiang 315211, China.
Apoptosis preserves organismal homeostasis by selectively eliminating unnecessary or damaged cells, with accumulating evidence also suggesting that it activates regenerative pathways and facilitates tissue remodeling. To date, however, the regulatory mechanisms linking this form of programmed cell death to regeneration remain poorly defined, particularly in evolutionarily basal organisms. Using the sea cucumber ( ) as a model for intestinal regeneration, this study identified robust apoptotic activity across key regenerative stages.
View Article and Find Full Text PDFIntegrated Metabolomics Using Data-Dependent Acquisition and Data-Independent Acquisition and Network Pharmacology to Reveal the Mechanisms of Usnic Acid in Treating Non-Small Cell Lung Cancer.
Chem Biodivers
September 2025
Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, People's Republic of China.
Usnic acid, a compound from Usneae Filum, has shown notable antitumor effects. Nevertheless, the mechanism of its anti-NSCLC action remains incompletely elucidated. This study used metabolomics, network pharmacology, molecular docking, and dynamics simulation to investigate usnic acid's potential mechanism on NSCLC utilizing A549 cell samples.
View Article and Find Full Text PDFNavigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools.
J Vis Exp
August 2025
Molemuse Biotech Studio;
Mass spectrometry (MS)-based proteomics data, including Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA), are widely used in biological research. However, the application of these datasets in validation studies is still limited due to the lack of clear demonstrations on how to effectively search and analyze proteomic data. To fill this gap, we selected one DDA and one DIA dataset deposited in the PRoteomics IDEntifications Database (PRIDE) data repository to better illustrate the proteomic data analysis workflow and downstream post-processing of protein search results.
View Article and Find Full Text PDFDIA-based proteomics reveals anti-inflammatory role of DL-3--butylphthalide in cerebral small vessel disease-induced brain injury in hypertensive rat.
Transl Neurosci
January 2025
Department of Neurology, Hebei General Hospital, Shijiazhuang, Hebei, P.R. China.
Objectives: Excessive neuroinflammatory responses represent a key pathological mechanism in cerebral small vessel disease (CSVD). Dl-3--butylphthalide (NBP), a compound previously demonstrated to possess anti-inflammatory properties in ischemic stroke, was investigated for its potential therapeutic effects in a rodent model of CSVD. This study aimed to elucidate the neuroprotective mechanisms of NBP in CSVD pathogenesis.
View Article and Find Full Text PDF