Article
Biochemical Research Methods
Chengwen Wen, Xiurong Wu, Guanzhong Lin, Wei Yan, Guohong Gan, Xiao Xu, Xiang-Yu Chen, Xi Chen, Xianming Liu, Guo Fu, Chuan-Qi Zhong
Summary: This study compares four commonly used DDA library-free approaches for analyzing phosphoproteomics and ubiquitinomics DIA MS data, revealing Spectronaut's directDIA as the top performer for phosphopeptide detection and an in silico-predicted library based on DIA-NN as the best option for ubiquitinomics diaPASEF data analysis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Yaoting Sun, Lu Li, Yan Zhou, Weigang Ge, He Wang, Runxin Wu, Wei Liu, Hao Chen, Qi Xiao, Xue Cai, Zhen Dong, Fangfei Zhang, Junhong Xiao, Guangzhi Wang, Yi He, Jinlong Gao, Oi Lian Kon, Narayanan Gopalakrishna Iyer, Haixia Guan, Xiaodong Teng, Yi Zhu, Yongfu Zhao, Tiannan Guo
Summary: Thyroid nodules are common in about 60% of the population. Differentiating between follicular adenoma (FA) and carcinoma (FTC) is a challenge in thyroid nodule diagnosis. This study presents a comprehensive thyroid spectral library and identifies nine proteins that could potentially distinguish FA and FTC.
MOLECULAR ONCOLOGY
(2022)
Article
Biochemical Research Methods
Lilian R. Heil, William E. Fondrie, Christopher D. McGann, Alexander J. Federation, William S. Noble, Michael J. MacCoss, Uri Keich
Summary: This study presents a new approach for peptide detection, generating spectral libraries directly from DIA mass spectrometry data and successfully detecting phosphorylated peptides. The method is competitive in accuracy and sensitivity compared to other library-free approaches.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Marc Isaksson, Christofer Karlsson, Thomas Laurell, Agnete Kirkeby, Moritz Heusel
Summary: Data-independent acquisition-mass spectrometry (DIA-MS) is the method of choice for deep, consistent, and accurate single-shot profiling in bottom-up proteomics. Library-free approaches based on in silico prediction promise deep DIA-MS profiling with reduced experimental effort and cost, but coverage and sensitivity in such analyses are limited.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Patrick Willems, Ursula Fels, An Staes, Kris Gevaert, Petra Van Damme
Summary: To study physiological responses in bacterial infections, an optimized hybrid library generation workflow for DIA mass spectrometry was found to significantly improve sensitivity and depth of protein detection, without the need for prior enrichment of bacterial pathogens.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Oncology
Liujia Qian, Jianqing Zhu, Zhangzhi Xue, Tingting Gong, Nan Xiang, Liang Yue, Xue Cai, Wangang Gong, Junjian Wang, Rui Sun, Wenhao Jiang, Weigang Ge, He Wang, Zhiguo Zheng, Qijun Wu, Yi Zhu, Tiannan Guo
Summary: High-grade serous ovarian carcinoma (HGSOC) is a common subtype of ovarian cancer with low survival rates. Neoadjuvant chemotherapy (NACT) followed by interval debulking surgery (IDS) is recommended for advanced-stage HGSOC patients. However, a significant number of patients exhibit chemoresistance with unknown mechanisms.
MOLECULAR ONCOLOGY
(2023)
Article
Biochemical Research Methods
Carolyn Allen, Rico Meinl, J. Sebastian Paez, Brian C. Searle, Seth Just, Lindsay K. Pino, William E. Fondrie
Summary: This study presents an open-source NextFlow pipeline, nf-encyclopedia, which connects three open-source tools (MSConvert, EncyclopeDIA, and MSstats) for analyzing DIA proteomics experiments with or without chromatogram libraries. The pipeline is reproducible and provides robust peptide and protein quantification. MSstats improves protein-level quantification performance over EncyclopeDIA alone.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Pavel Sinitcyn, Hamid Hamzeiy, Favio Salinas Soto, Daniel Itzhak, Frank McCarthy, Christoph Wichmann, Martin Steger, Uli Ohmayer, Ute Distler, Stephanie Kaspar-Schoenefeld, Nikita Prianichnikov, Sule Yilmaz, Jan Daniel Rudolph, Stefan Tenzer, Yasset Perez-Riverol, Nagarjuna Nagaraj, Sean J. Humphrey, Jurgen Cox
Summary: MaxDIA is a software platform specifically designed for analyzing DIA proteomics data within the MaxQuant environment, achieving deep proteome coverage and improved protein quantification accuracy. It provides accurate FDR estimates for hypothesis-free analysis of DIA samples.
NATURE BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Jen-Hung Wang, Wai-Kok Choong, Ching-Tai Chen, Ting-Yi Sung
Summary: This article introduces a spectral library search tool called Calibr for spectrum-centric DIA data analysis. Calibr improves the number of spectrum-spectrum matches and peptides compared to traditional preprocessing methods. When compared to DDA and MassIVE spectral libraries, Calibr also demonstrates higher sensitivity.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Analytical
Asad Ali Siyal, Eric Sheng-Wen Chen, Hsin-Ju Chan, Reta Birhanu Kitata, Jhih-Ci Yang, Hsiung-Lin Tu, Yu-Ju Chen
Summary: The study presents a sample size-comparable library-based DIA approach, achieving higher protein group identification from small-size library compared to medium-size, large-size, and lung cancer resource spectral library. The approach shows good generality across different instruments and data analysis methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Selvam Paramasivan, Janna L. Morrison, Mitchell C. Lock, Jack R. T. Darby, Roberto A. Barrero, Paul C. Mills, Pawel Sadowski
Summary: Sequential window acquisition of all theoretical mass spectra-mass spectrometry, supported by advanced bioinformatics, provides a comprehensive framework for proteome analysis and biomarker discovery. However, the lack of a generic sample preparation platform for heterogeneous materials from different sources limits its broad application. We developed universal and fully automated workflows using a robotic sample preparation platform, enabling in-depth and reproducible proteome coverage of bovine and ovine specimens. The high correlation between sheep proteomics and transcriptomics datasets validates this development and suggests the potential for various clinical applications across different animal species and disease models.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Shawn J. Rice, Chandra P. Belani
Summary: This study established a gas-phase fractionation (GPF) workflow for creating DIA libraries. The GPF workflow outperformed the traditional ddaPASEF workflow in identifying and quantifying proteins in plasma samples from nonsmall cell lung cancer patients. Overall, the choice of DIA library workflow had a limited effect on the overall outcome of a plasma proteomics experiment, but it did affect the number of proteins identified and the total experiment time.
Article
Biotechnology & Applied Microbiology
Kriti Awasthi, Chinmaya Narayana Kootimole, Anjana Aravind, Thottethodi Subrahmanya Keshava Prasad
Summary: Currently, mass spectrometry-based data-dependent acquisition protocols require significant amounts of proteins and complex protocols to identify low abundant proteins. Data-independent acquisition (DIA) approach allows identification of numerous proteins irrespective of their abundance, making it important for studying biological systems where protein availability is limited. In this study, a spectral library for Mycobacterium tuberculosis proteome was generated using publicly available proteomic data sets, providing a valuable resource for researchers studying M. tuberculosis using DIA approaches.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)
Article
Biochemical Research Methods
Chris D. McGann, William D. Barshop, Jesse D. Canterbury, Chuwei Lin, Wassim Gabriel, Jingjing Huang, David Bergen, Vlad Zabrouskov, Rafael D. Melani, Mathias Wilhelm, Graeme C. McAlister, Devin K. Schweppe
Summary: Sample multiplexed quantitative proteomics assays have improved instrument efficiency and quantitative accuracy through the development of intelligent data acquisition (IDA) strategies. The implementation of a real-time spectral library searching (RTLS) workflow enables intelligent scan triggering and peak selection in milliseconds, leading to improved quantitation of multiplexed samples. The RTLS method expands the IDA toolbox and allows for more efficient and accurate analysis of molecular phenotypes.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Aparna Srinivasan, Justin C. Sing, Anne-Claude Gingras, Hannes L. Rost
Summary: Mass spectrometry-based profiling of the phosphoproteome is a powerful method for identifying phosphorylation events. This Perspective reviews recent studies comparing data-dependent acquisition (DDA) and data-independent acquisition (DIA) methods for phosphoproteomics and discusses data analysis options. The analysis of a phosphopeptide-enriched data set shows that DDA identifies more unique phosphopeptides, while DIA provides more consistent identifications across replicates. Challenges include identifying coeluting phosphopeptide isomers and reproducibly locating high-confidence phosphorylation sites.
JOURNAL OF PROTEOME RESEARCH
(2022)
