iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control by Huanhuan Gao, Yi Zhu, Dongxue Wang, Zongxiang Nie, He Wang, Guibin Wang, Shuang Liang, Yuting Xie, Yingying Sun, Wenhao Jiang, Zhen Dong, Liqin Qian, Xufei Wang, Mengdi Liang, Min Chen, Houqi Fang, Qiufang Zeng, Jiao Tian, Zeyu Sun, Juan Xue, Shan Li, Chen Chen, Xiang Liu, Xiaolei Lyu, Zhenchang Guo, Yingzi Qi, Ruoyu Wu, Xiaoxian Du, Tingde Tong, Fengchun Kong, Liming Han, Minghui Wang, Yang Zhao, Xinhua Dai, Fuchu He, Tiannan Guo

“…Here, we collect 2754 files acquired by data independent acquisition (DIA) and paired 2638 DDA files from mouse liver digests using 21 mass spectrometers across nine laboratories over 31 months. …”
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Proteome differences of dental stem cells between permanent and deciduous teeth by data-independent acquisition proteomics by Zhang Suping, Liu Yuqing, Dong Jin, Jiao Min, Gu Yongchun, Chen Liling, Yuan Na, Wang Jianrong, Yang Dezhao, Meng Fanwen

“…To address this gap, we employed a novel data-independent acquisition (DIA) proteomics approach to compare the protein expression profiles of DPSC and SHED. …”
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Cross-sectional study of proteomic differences between moderate and severe psoriasis by Lingling Wu, Chen Cen, Bibo Xie, Lihua Hu, Jia Huang, Ningning Shen, Qiang Dong

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diaTracer enables spectrum-centric analysis of diaPASEF proteomics data by Kai Li, Guo Ci Teo, Kevin L. Yang, Fengchao Yu, Alexey I. Nesvizhskii

“…The integration of ion mobility separation into data-independent acquisition analysis, such as the diaPASEF technology available on Bruker’s timsTOF platform, further improves the quantification accuracy and protein depth achievable using data-independent acquisition. …”
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Don't die like me: Which proteins are responsible for the selective neuronal vulnerability within the substantia nigra? by Simone Steinbach, Mariana Molina, Lea T Grinberg, Luisa Aring, Annika Guntermann, Katrin Marcus, Helmut Heinsen, Renata E Paraizo Leite, Caroline May

“…Following, their proteome was analyzed by data independent acquisition mass spectrometry. The samples were analysed donor-specifically and not pooled for this purpose. …”
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Anaplasma phagocytophilum AFAP targets the host nucleolus and inhibits induced apoptosis by Daxiu Zhang, Lifeng Yu, Hui Tang, Hua Niu, Hua Niu, Hua Niu

“…A total of 586 host proteins were identified interacting with AFAP by data-independent acquisition mass spectrometry and annotated to 501 Gene Ontology (GO) terms, with the significantly over-represented ones related to ribosomes, nucleolus, DNA binding, and rRNA metabolic process. …”
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Proteomic analysis of egg production peak and senescence in the ovaries of Taihe black-boned silky fowl (Gallus gallus domesticus Brisson) by Xuan Huang, Shibao Li, Yuting Tan, Chunhui Xu, Yunyan Huang, Zhaozheng Yin

“…In this research endeavor, we employed an advanced, rapid DIA (Data independent acquisition) quantitative proteomics method on the Astral platform to meticulously analyze the ovarian proteome of these chickens. …”
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The pathomechanism of bone marrow edema in the femoral head necrosis with pericollapse stage by Liang Mo, Zhangzheng Wang, Mengyu Jiang, Chi Zhou, Chao Ma, Yinuo Fan, Wei He, Zhenqiu Chen, Yuhao Liu

“…Meanwhile, data-independent Acquisition (DIA) proteomics technology was utilized to identify differentially expressed proteins (DEPs) within bone tissue. 141, 299 and 852 DEPs were identified in femoral neck, necrotic and sclerotic regions, respectively. …”
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Changes in the rhizosphere metabolome profile of wastewater-irrigated lettuces (Lactuca sativa L.) highlighted using non-target HRMS and ROIMCR chemometrics method by Carlos Pérez-López, Lúcia H.M.L.M. Santos, Antoni Ginebreda, Lucas L. Alonso, Gianluigi Buttiglieri, Evangelos Statiris, Damia Barcelo, Sara Rodriguez-Mozaz, Roma Tauler

“…Samples were collected from the rhizosphere soil of the lettuces and were analyzed using Liquid Chromatography – High-Resolution Mass Spectrometry (LC-HRMS) with Data-Independent Acquisition (DIA). Non-target metabolomic profiling was performed using the Regions of Interest procedure (ROI), followed by Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) for simultaneous analysis of MS1 and MS2 signals in positive and negative ionization modes. …”
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Mapping Nanoscale‐To‐Single‐Cell Phosphoproteomic Landscape by Chip‐DIA by Gul Muneer, Sofani Tafesse Gebreyesus, Ciao‐Syuan Chen, Tzu‐Tsung Lee, Fengchao Yu, Chih‐An Lin, Min‐Shu Hsieh, Alexey I. Nesvizhskii, Chao‐Chi Ho, Sung‐Liang Yu, Hsiung‐Lin Tu, Yu‐Ju Chen

“…Here, we present a Chip‐DIA strategy, integrating a microfluidic‐based phosphoproteomic chip (iPhosChip) with data‐independent acquisition mass spectrometry (DIA‐MS) for ultrasensitive nanoscale‐to‐single‐cell phosphoproteomic profiling. …”
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Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics by Xiang Liu, Haidan Sun, Xinhang Hou, Jiameng Sun, Min Tang, Yong-Biao Zhang, Yongqian Zhang, Wei Sun, Chao Liu, Urine Test Sample Working Group

“…Our study involves 20 LC-MS platforms and reveals that, when combined with a comprehensive QC system and a unified SOP, the data generated by data-independent acquisition (DIA) workflow in urine QC samples exhibit high robustness, sensitivity, and reproducibility across multiple LC-MS platforms. …”
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Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics by George S. Biggs, Emma E. Cawood, Aini Vuorinen, William J. McCarthy, Harry Wilders, Ioannis G. Riziotis, Antonie J. van der Zouwen, Jonathan Pettinger, Luke Nightingale, Peiling Chen, Andrew J. Powell, David House, Simon J. Boulton, J. Mark Skehel, Katrin Rittinger, Jacob T. Bush

“…This high-throughput platform combines SP4 plate-based sample preparation with rapid chromatographic gradients. Data-independent acquisition performed on a Bruker timsTOF Pro 2 consistently identified ~23,000 cysteine sites per run, with a total of ~32,000 cysteine sites profiled in HEK293T and Jurkat lysate. …”
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DIA-based quantitative proteomic analysis on porcine meat quality at different chilling rates by Yuqiang Bai, Tongjing Yan, Fei Fang, Xin Li, Su Wang, Juan Li, Chengli Hou, Dequan Zhang

“…The objective of this study was to evaluate the effects of chilling rate on porcine meat quality from the perspective of proteome using data independent acquisition (DIA)-based quantitative proteomic strategy. …”
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Gas-phase fractionation DDA promotes in-depth DIA phosphoproteome analysis by Zhiwei Tu, Yabin Li, Shuhui Ji, Shanshan Wang, Rui Zhou, Gertjan Kramer, Yu Cui, Fei Xie

“…Data-independent acquisition (DIA) is a promising method for quantitative proteomics. …”
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Research on screening key proteins related to the pathogenesis of sepsis associated encephalopathy based on DIA proteomics technology by Wu Shuhui, Hu Hongjie, Lu Yuru, Zhu Wei

“…Objective To explore the key proteins in plasma of patients with sepsis associated encephalopathy (SAE) through data-independent acquisition(DIA) quantitative proteomics and machine learning techniques, with the aim of guiding research on SAE pathogenesis and aiding early diagnosis. …”
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Plasma prolactin axis shift from placental to pituitary origin in late prepartum mice by Taku James Sairenji, Shinnosuke Masuda, Yuya Higuchi, Mitsue Miyazaki, Hiroyuki Yajima, Oh Kwan Ee, Yuki Fujiwara, Takuya Araki, Noriaki Shimokawa, Noriyuki Koibuchi

“…To investigate this hypothesis and to seek proteomic changes, we performed a shotgun proteome analysis of the placental tissue using data-independent acquisition mass spectrometry (DIA-MS). Up to 5,891 proteins were identified, including 17 PRL family members. …”
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Depot-specific acetylation profiles of adipose tissues—therapeutic targets for metabolically unhealthy obesity by Haoyue Guo, Zhiyi Zhang, Juntao Yang, Jiangfeng Liu, Hongwei Lin, Ningbei Yin

“…Methods Paired omental VA and abdominal SA samples were obtained from four male patients with MUO and subjected to Four-Dimensional Data Independent Acquisition (4D-DIA) proteomic and lysine acetylation (Kac) analyses. …”
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