Article
Biochemical Research Methods
Dongyoon Shin, Sang Jin Rhee, Jihyeon Lee, Injoon Yeo, Misol Do, Eun-Jeong Joo, Hee Yeon Jung, Sungwon Roh, Sang-Hyuk Lee, Hyeyoung Kim, Minji Bang, Kyu Young Lee, Jun Soo Kwon, Kyooseob Ha, Yong Min Ahn, Youngsoo Kim
Summary: This study successfully differentiated major depressive disorder (MDD) from bipolar disorder (BD) using a targeted proteomic approach, developing a model composed of nine proteins with good discriminative ability. The proteins identified were associated with neuro, oxidative/nitrosative stress, and immunity/inflammation-related biological functions.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Claudia Gaither, Robert Popp, Sophia P. Borchers, Kjartan Skarphedinsson, Finnur F. Eiriksson, Margret Thorsteinsdottir, Yassene Mohammed, Christoph H. Borchers
Summary: The study demonstrated that leaving a lyophilized peptide mixture at room temperature for up to 20 days does not affect the quantitative performance of mass spectrometry analysis, making it a feasible option for sample transportation. Most peptide concentrations showed minimal fluctuations across different time points, indicating the stability of the peptide mixture under the tested conditions.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Maura Brioschi, Erica Gianazza, Piergiuseppe Agostoni, Beatrice Zoanni, Alice Mallia, Cristina Banfi
Summary: This study used a targeted mass spectrometry approach to analyze plasma samples from HF patients and healthy controls, identifying a panel of four plasma proteins associated with HF severity and pulmonary dysfunction, with the potential to distinguish between HF patients and healthy subjects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Niko Pinter, Damian Glaetzer, Matthias Fahrner, Klemens Frohlich, James Johnson, Bjoern Andreas Gruening, Bettina Warscheid, Friedel Drepper, Oliver Schilling, Melanie Christine Foell
Summary: Quantitative mass spectrometry-based proteomics is a high-throughput technology for identifying and quantifying proteins in complex samples. Researchers have integrated MaxQuant and MSstats into the open-source Galaxy framework, enabling accessible and reproducible proteomics analysis in a cloud environment. This integration can be combined with thousands of existing Galaxy tools, providing the foundation for high-throughput proteomics data science for everyone.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Devon Kohler, Mateusz Staniak, Tsung-Heng Tsai, Ting Huang, Nicholas Shulman, Oliver M. Bernhardt, Brendan X. MacLean, Alexey I. Nesvizhskii, Lukas Reiter, Eduard Sabido, Meena Choi, Olga Vitek
Summary: The MSstats R-Bioconductor family of packages, particularly the new version MSstats v4.0, is widely used for statistical analyses of quantitative proteomic experiments. It provides improved usability, versatility, and accuracy of statistical methodology, as well as better memory use and computation speed. Empirical comparisons have demonstrated the stronger performance and better usability of MSstats v4.0 compared to existing methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana B. Bravo, Maria del Pilar Chantada-Vazquez, Ruben Varela-Fernandez, Paulo Avila-Gomez, Pablo Hervella, Isabel Lema
Summary: Utilizing SWATH-MS for tear protein quantification, dysregulated proteins involved in iron homeostasis, inflammatory-immune response, oxidative stress, and other biological processes were identified in patients with keratoconus. The study sheds light on the molecular mechanisms underlying the disease and highlights the potential therapeutic targets related to iron accumulation and tissue damage in keratoconus pathophysiology.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Biochemical Research Methods
Nicole M. Hartung, Annika I. Ostermann, Stephan Immenschuh, Nils Helge Schebb
Summary: This study presents a targeted proteomics method for human COX-2, allowing simultaneous monitoring of gene expression levels and investigation of COX-2's role in human colon carcinoma cell lines and lipopolysaccharide-stimulated human primary macrophages. The developed methodology aims to be a standard operation procedure for comprehensive targeted proteomics/oxylipin metabolomics strategies in examining the arachidonic acid cascade.
Article
Biochemical Research Methods
Hyojin Kim, Dong Huey Cheon, Won Suk Yang, Je-Hyun Baek
Summary: This study developed a protein-MRM method without digestion to individually quantify APOC-III proteoforms in human serum. The method provides an affordable and rapid quantification of potential disease-specific proteoforms and allows investigators to identify novel biological roles potentially related to cardiovascular disease or novel biomarkers.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biology
Jonathan G. Van Vranken, Jiaming Li, Dylan C. Mitchell, Jose Navarrete-Perea, Steven P. Gygi
Summary: Recent advances in mass spectrometry have enabled quantitative proteomics to become a powerful tool in drug discovery, with the development of solvent shift assays allowing for the establishment of target engagement and increased efficiency. Using this approach, specific targets of compounds with known mechanisms of action can be readily identified, and combining solvent proteome profiling with other methods can expand the screening capabilities for evidence of ligand binding in the proteome.
Review
Oncology
Arada Vinaiphat, Jee Keem Low, Kheng Wei Yeoh, Wee Joo Chng, Siu Kwan Sze
Summary: Cancer, as a major contributor to global chronic disease burden, is closely related to low-oxygen stress. Traditional proteomic approaches have been used to study cancer mechanisms associated with oxygen deprivation, but clinical therapeutic outcomes have been limited. Therefore, the development of new strategies and technologies is crucial for multi-target drug discovery.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemical Research Methods
Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu
Summary: This study introduces a new storage format called mzMD for MS datasets and presents an algorithm to query this format for summarizing a given data window. Experimental results demonstrate the high speed and stability of mzMD in retrieving high-quality data window summaries.
Article
Chemistry, Medicinal
Faith O. Osinaga, Yu-Chih Chen, Madan K. Kharel, Yan Waguespack, Sichu Li, Shaochung Victor Hsia
Summary: The study investigates the production of GHB during HSV-1 infection and its biochemical pathways. UV-inactivation of HSV-1 reduces GHB production, while ACV or CHX treatments have no effect. Inhibition of glycolysis activity by NaF also decreases GHB production. The findings suggest that early events following infection modulate the release of GHB through the metabolic pathways of glycolysis and TCA cycle.
Article
Cell Biology
Tian-Yi Zhu, Shang-Tong Li, Dan-Dan Liu, Xiajun Zhang, Lianqi Zhou, Rong Zhou, Bing Yang
Summary: This study quantifies protein changes during aging in different individuals using single-worm mass spectrometry, and reveals the heterogeneity of aging by reconstructing the aging trajectory and proteomic landscape of C. elegans.
Article
Multidisciplinary Sciences
Kevin L. Yang, Fengchao Yu, Guo Ci Teo, Kai Li, Vadim Demichev, Markus Ralser, Alexey I. Nesvizhskii
Summary: This article presents an accessible method to improve peptide spectrum match rescoring using deep learning predictions in bottom-up proteomics. The authors demonstrate significant improvements in peptide/protein identifications across various experiments, including single-cell proteomics and immunopeptidomics. They introduce a new tool called MSBooster, which incorporates deep learning-based predictions of peptide properties to rescore peptide-to-spectrum matches, and show its utility in different workflows, such as immunopeptidomics and single-cell proteomics.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Alexey S. Kononikhin, Natalia Zakharova, Savva D. Semenov, Anna E. Bugrova, Alexander G. Brzhozovskiy, Maria I. Indeykina, Yana B. Fedorova, Igor Kolykhalov, Polina A. Strelnikova, Anna Yu Ikonnikova, Dmitry A. Gryadunov, Svetlana Gavrilova, Evgeny N. Nikolaev
Summary: Early recognition of Alzheimer's disease onset is a global challenge. This study used proteomic analysis to confirm a panel of consistent protein markers associated with AD, providing a potential method for reliable screening.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Hasmik Keshishian, Michael W. Burgess, Michael A. Gillette, Philipp Mertins, Karl R. Clauser, D. R. Mani, Eric W. Kuhn, Laurie A. Farrell, Robert E. Gerszten, Steven A. Carr
MOLECULAR & CELLULAR PROTEOMICS
(2015)
Article
Biochemical Research Methods
Susan E. Abbatiello, Birgit Schilling, D. R. Mani, Lisa J. Zimmerman, Steven C. Hall, Brendan Maclean, Matthew Albertolle, Simon Allen, Michael Burgess, Michael P. Cusack, Mousumi Gosh, Victoria Hedrick, Jason M. Held, H. Dorota Inerowicz, Angela Jackson, Hasmik Keshishian, Christopher R. Kinsinger, John Lyssand, Lee Makowski, Mehdi Mesri, Henry Rodriguez, Paul Rudnick, Pawel Sadowski, Nell Sedransk, Kent Shaddox, Stephen J. Skates, Eric Kuhn, Derek Smith, Jeffery R. Whiteaker, Corbin Whitwell, Shucha Zhang, Christoph H. Borchers, Susan J. Fisher, Bradford W. Gibson, Daniel C. Liebler, Michael J. MacCoss, Thomas A. Neubert, Amanda G. Paulovich, Fred E. Regnier, Paul Tempst, Steven A. Carr
MOLECULAR & CELLULAR PROTEOMICS
(2015)
Article
Chemistry, Analytical
Paul J. Ippoliti, Eric Kuhn, D. R. Mani, Lola Fagbami, Hasmik Keshishian, Michael W. Burgess, Jacob D. Jaffe, Steven A. Carr
ANALYTICAL CHEMISTRY
(2016)
Article
Biochemistry & Molecular Biology
Hui Zhang, Tao Liu, Zhen Zhang, Samuel H. Payne, Bai Zhang, Jason E. McDermott, Jian-Ying Zhou, Vladislav A. Petyuk, Li Chen, Debjit Ray, Shisheng Sun, Feng Yang, Lijun Chen, Jing Wang, Punit Shah, Seong Won Cha, Paul Aiyetan, Sunghee Woo, Yuan Tian, Marina A. Gritsenko, Therese R. Clauss, Caitlin Choi, Matthew E. Monroe, Stefani Thomas, Song Nie, Chaochao Wu, Ronald J. Moore, Kun-Hsing Yu, David L. Tabb, David Fenyo, Vineet Bafna, Yue Wang, Henry Rodriguez, Emily S. Boja, Tara Hiltke, Robert C. Rivers, Lori Sokoll, Heng Zhu, Ie-Ming Shih, Leslie Cope, Akhilesh Pandey, Bing Zhang, Michael P. Snyder, Douglas A. Levine, Richard D. Smith, Daniel W. Chan, Karin D. Rodland
Article
Biochemical Research Methods
Jacob D. Jaffe, Caitlin M. Feeney, Jinal Patel, Xiaodong Lu, D. R. Mani
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2016)
Article
Multidisciplinary Sciences
Philipp Mertins, D. R. Mani, Kelly V. Ruggles, Michael A. Gillette, Karl R. Clauser, Pei Wang, Xianlong Wang, Jana W. Qiao, Song Cao, Francesca Petralia, Emily Kawaler, Filip Mundt, Karsten Krug, Zhidong Tu, Jonathan T. Lei, Michael L. Gatza, Matthew Wilkerson, Charles M. Perou, Venkata Yellapantula, Kuan-lin Huang, Chenwei Lin, Michael D. McLellan, Ping Yan, Sherri R. Davies, R. Reid Townsend, Steven J. Skates, Jing Wang, Bing Zhang, Christopher R. Kinsinger, Mehdi Mesri, Henry Rodriguez, Li Ding, Amanda G. Paulovich, David Fenyo, Matthew J. Ellis, Steven A. Carr
Review
Biochemical Research Methods
Kelly V. Ruggles, Karsten Krug, Xiaojing Wang, Karl R. Clauser, Jing Wang, Samuel H. Payne, David Fenyo, Bing Zhang, D. R. Mani
MOLECULAR & CELLULAR PROTEOMICS
(2017)
Editorial Material
Biochemical Research Methods
Susan Abbatiello, Bradley L. Ackermann, Christoph Borchers, Ralph A. Bradshaw, Steven A. Carr, Robert Chalkley, Meena Choi, Eric Deutsch, Bruno Domon, Andrew N. Hoofnagle, Hasmik Keshishian, Eric Kuhn, Daniel C. Liebler, Michael MacCoss, Brendan MacLean, D. R. Mani, Hendrik Neubert, Derek Smith, Olga Vitek, Lisa Zimmerman
MOLECULAR & CELLULAR PROTEOMICS
(2017)
Article
Multidisciplinary Sciences
Kuan-lin Huang, Shunqiang Li, Philipp Mertins, Song Cao, Harsha P. Gunawardena, Kelly V. Ruggles, D. R. Mani, Karl R. Clauser, Maki Tanioka, Jerry Usary, Shyam M. Kavuri, Ling Xie, Christopher Yoon, Jana W. Qiao, John Wrobel, Matthew A. Wyczalkowski, Petra Erdmann-Gilmore, Jacqueline E. Snider, Jeremy Hoog, Purba Singh, Beifung Niu, Zhanfang Guo, Sam Qiancheng Sun, Souzan Sanati, Emily Kawaler, Xuya Wang, Adam Scott, Kai Ye, Michael D. McLellan, Michael C. Wendl, Anna Malovannaya, Jason M. Held, Michael A. Gillette, David Fenyo, Christopher R. Kinsinger, Mehdi Mesri, Henry Rodriguez, Sherri R. Davies, Charles M. Perou, Cynthia Ma, R. Reid Townsend, Xian Chen, Steven A. Carr, Matthew J. Ellis, Li Ding
NATURE COMMUNICATIONS
(2017)
Article
Multidisciplinary Sciences
Alexandra Naba, Karl R. Clauser, D. R. Mani, Steven A. Carr, Richard O. Hynes
SCIENTIFIC REPORTS
(2017)
Article
Oncology
Filip Mundt, Sandeep Rajput, Shunqiang Li, Kelly V. Ruggles, Arshag D. Mooradian, Philipp Mertins, Michael A. Gillette, Karsten Krug, Zhanfang Guo, Jeremy Hoog, Petra Erdmann-Gilmore, Tina Primeau, Shixia Huang, Dean P. Edwards, Xiaowei Wang, Xuya Wang, Emily Kawaler, D. R. Mani, Karl R. Clauser, Feng Gao, Jingqin Luo, Sherri R. Davies, Gary L. Johnson, Kuan-Lin Huang, Christopher J. Yoon, Li Ding, David Fenyoe, Matthew J. Ellis, R. Reid Townsend, Jason M. Held, Steven A. Carr, Cynthia X. Ma
Article
Biochemistry & Molecular Biology
Rajiv K. Khajuria, Mathias Munschauer, Jacob C. Ulirsch, Claudia Fiorini, Leif S. Ludwig, Sean K. McFarland, Nour J. Abdulhay, Harrison Specht, Hasmik Keshishian, D. R. Mani, Marko Jovanovic, Steven R. Ellis, Charles P. Fulco, Jesse M. Engreitz, Sabina Schutz, John Lian, Karen W. Gripp, Olga K. Weinberg, Geraldine S. Pinkus, Lee Gehrke, Aviv Regev, Eric S. Lander, Hanna T. Gazda, Winston Y. Lee, Vikram G. Panse, Steven A. Carr, Vijay G. Sankaran
Article
Biochemical Research Methods
Philipp Mertins, Lauren C. Tang, Karsten Krug, David J. Clark, Marina A. Gritsenko, Lijun Chen, Karl R. Clauser, Therese R. Clauss, Punit Shah, Michael A. Gillette, Vladislav A. Petyuk, Stefani N. Thomas, D. R. Mani, Filip Mundt, Ronald J. Moore, Yingwei Hui, Rui Zhao, Michael Schnaubelt, Hasmik Keshishian, Matthew E. Monroe, Zhen Zhang, Namrata D. Udeshi, Deepak Mani, Sherri R. Davies, R. Reid Townsend, Daniel W. Chan, Richard D. Smith, Hui Zhang, Tao Liu, Steven A. Carr
Letter
Biochemical Research Methods
D. R. Mani, Myranda Maynard, Ramani Kothadia, Karsten Krug, Karen E. Christianson, David Heiman, Karl R. Clauser, Chet Birger, Gad Getz, Steven A. Carr
Review
Oncology
D. R. Mani, Karsten Krug, Bing Zhang, Shankha Satpathy, Karl R. Clauser, Li Ding, Matthew Ellis, Michael A. Gillette, Steven A. Carr
Summary: Genomic analyses have greatly impacted cancer research by identifying driver mutations and developing targeted therapies. However, the functions of most somatic mutations and copy number variants in tumors remain unknown. Proteogenomics, which integrates proteins and their modifications with genomic data, has emerged as a new field and is providing valuable insights into malignant transformation and therapeutic outcomes.
NATURE REVIEWS CANCER
(2022)