Article
Biology
Matthias Fahrner, Melanie Christine Foll, Bjorn Andreas Gruning, Matthias Bernt, Hannes Rost, Oliver Schilling
Summary: The integration of an open-source DIA analysis suite in the web-based and user-friendly Galaxy framework, along with comprehensive training materials, enables a wide community of researchers to perform reproducible and transparent DIA data analysis.
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
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)
Article
Biochemistry & Molecular Biology
Anzhong Huang, Wei Wu, Song Chen, Hanbing Hu, Jie Shen, Jingbo Qie, Ming Zhong, Lin Zhang
Summary: This study investigated the proteomic changes in the human intestine during intestinal ischemia-reperfusion (II/R) injury. The results identified several differentially expressed proteins (DEPs) between II/R and control samples, and demonstrated the potential roles of FLNA and MYL9 in the progress of II/R injury.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(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)
Review
Chemistry, Analytical
Haoyue Zhang, Zheng Ouyang, Wenpeng Zhang
Summary: This article reviews the recent development of MS bioinformatics in clinical analysis, focusing on data acquisition, interpretation, and integration. It also discusses the future development of MS bioinformatics in addressing current clinical challenges.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Shuang Weng, Mingchao Wang, Yingyi Zhao, Wantao Ying, Xiaohong Qian
Summary: The study established a high-coverage HCC spectral library and optimized the DIA method for large-scale quantitative proteomics analysis of HCC clinical samples. The optimized one-shot DIA approach could reach a similar identification compared to multi-fraction DDA while consuming shorter acquisition time, paving the way for analyzing thousands of clinical samples.
JOURNAL OF PROTEOMICS
(2021)
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
Chemistry, Analytical
Lilian R. Heil, Philip M. Remes, Jesse D. Canterbury, Ping Yip, William D. Barshop, Christine C. Wu, Michael J. MacCoss
Summary: Data-independent acquisition (DIA) mass spectrometry has become popular due to its reproducibility and quantitative rigor. However, traditional DIA methods may waste instrument time acquiring MS/MS spectra with no usable information. We developed a dynamic DIA strategy that improves quantification sensitivity without sacrificing the number of detected peptides.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Syed Muhammad Zaki Shah, Arslan Ali, Muhammad Noman Khan, Adeeba Khadim, Mufarreh Asmari, Jalal Uddin, Syed Ghulam Musharraf
Summary: In this study, we proposed a pipeline for quantitative profiling of pharmaceutical drugs and serum metabolites in DIA mode. The results showed that the constructed workflow had remarkable analytical performance, making it a sensitive and reproducible pipeline for biological complex fluids.
Article
Biochemistry & Molecular Biology
Rosalie Nijssen, Marco H. Blokland, Robin S. Wegh, Erik de Lange, Stefan P. J. van Leeuwen, Bjorn J. A. Berendsen, Milou G. M. van de Schans
Summary: Liquid chromatography combined with high-resolution mass spectrometry (LC-HRMS) is commonly used for suspect screening (SS) and non-target screening (NTS) in metabolomics and environmental toxicology. This study evaluated the performance of four HRMS-spectra identification tools for annotating HRMS spectra of 32 pesticides, veterinary drugs, and their metabolites. The study found that the identification success rates varied among different tools, with mzCloud and MSfinder performing well in DDA spectra and MSfinder performing the best in DIA spectra. The study also demonstrated that DIA spectra can be used for compound annotation in certain software tools, although the success rate is lower than for DDA spectra.
Article
Biochemical Research Methods
Leon Bichmann, Shubham Gupta, George Rosenberger, Leon Kuchenbecker, Timo Sachsenberg, Phil Ewels, Oliver Alka, Julianus Pfeuffer, Oliver Kohlbacher, Hannes Rost
Summary: DIA is a leading analysis method in biomedical mass spectrometry with advantages such as reproducibility and sensitivity, but its data analysis complexity requires expert knowledge. DIAproteomics is a multifunctional, automated pipeline that allows easy processing of DIA datasets.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Till-Hendrik Macher, Arne J. Beermann, Florian Leese
Summary: DNA metabarcoding is a powerful tool for biodiversity assessment, but analyzing and visualizing the data can be challenging for end users with limited bioinformatics expertise. TaxonTableTools (TTT) is a new GUI software that aims to bridge this gap by providing simple and reproducible workflows for analysis and visualization of DNA metabarcoding data, including various statistics and ecological analyses. The software is user-friendly and free to access through GitHub or the Python package index.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemical Research Methods
Yan Fang, Qing-Run Li, Zhen-Hang Zhang, Jia-Rui Wu, Hao-Ran Zheng, Rong Zeng
Summary: Data-independent acquisition (DIA) offers advantages for peptide quantification in mass spectrometry (MS), but mixed spectra present challenges for precise stoichiometry. This study introduces FIGS, a method for accurate and robust peptide quantification in DIA-MS data, by analyzing library spectra in specific sets and defining featured ions assigned to corresponding precursors. FIGS demonstrates high performance in quantification sensitivity, accuracy, and efficiency, significantly improving accuracy for the full dynamic range, especially low-abundance peptides.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Daniel A. Polasky, Daniel J. Geiszler, Fengchao Yu, Alexey I. Nesvizhskii
Summary: Recently, we introduced a fast and sensitive method for glycoproteomics search that can report glycopeptides with high confidence. We have also developed a new method for determining the glycan composition of N-linked glycopeptides fragmented by collisional or hybrid activation.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemical Research Methods
Heta S. Desai, Tianyang Yan, Fengchao Yu, Alexander W. Sun, Miranda Villanueva, Alexey I. Nesvizhskii, Keriann M. Backus
Summary: Proteinaceous cysteine residues are highly sensitive to oxidative stress, and understanding their relation to protein and cellular function is crucial for health and disease. Current mass spectrometry-based proteomic platforms provide insights into the redox proteome, but are limited by complicated sample preparation, expensive labeling reagents, and custom data analysis workflows. In this study, a new method called SP3-Rox is presented, which combines low-cost isotopically labeled capture reagents with SP3 sample cleanup for high throughput and high coverage identification of redox-sensitive cysteines.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Erpan Ahat, Sarah Bui, Jianchao Zhang, Felipe da Veiga Leprevost, Lisa Sharkey, Whitney Reid, Alexey I. Nesvizhskii, Henry L. Paulson, Yanzhuang Wang
Summary: This study investigates the unconventional protein secretion pathway mediated by Golgi reassembly stacking proteins (GRASPs) and identifies the mechanism of unconventional secretion for mutant huntingtin and other neurodegenerative disease-related proteins. The study also finds that GRASP55 levels are upregulated under stress conditions to facilitate unconventional secretion, and that inhibition of GRASP55-dependent secretion enhances mutant huntingtin aggregation and toxicity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Prabhodh S. Abbineni, Vi T. Tang, Felipe da Veiga Leprevost, Venkatesha Basrur, Jie Xiang, Alexey I. Nesvizhskii, David Ginsburg
Summary: By comparing the abundance of individual proteins between cell lysate and conditioned medium, it is possible to identify relatively more abundant secreted proteins in the conditioned medium. Treatment with brefeldin A confirmed the sensitivity and specificity of this approach, identifying candidates for unconventional secretion pathways.
ANALYTICAL BIOCHEMISTRY
(2022)
Article
Chemistry, Analytical
Junho Park, Fengchao Yu, James M. Fulcher, Sarah M. Williams, Kristin Engbrecht, Ronald J. Moore, Geremy C. Clair, Vladislav Petyuk, Alexey I. Nesvizhskii, Ying Zhu
Summary: To overcome the issue of ratio compression in isobaric labeling-based multiplexed single-cell proteomics, we developed an improved MS3-based method using a linear ion trap. This method increased proteome coverage for single-cell-level peptides and was applied to study immune activation in single macrophages.
ANALYTICAL CHEMISTRY
(2023)
Article
Oncology
Yize Li, Tung-Shing M. Lih, Saravana M. Dhanasekaran, Rahul Mannan, Lijun Chen, Marcin Cieslik, Yige Wu, Rita Jiu-Hsien Lu, David J. Clark, Iga Koodziejczak, Runyu Hong, Siqi Chen, Yanyan Zhao, Seema Chugh, Wagma Caravan, Nataly Naser Al Deen, Noshad Hosseini, Chelsea J. Newton, Karsten Krug, Yuanwei Xu, Kyung-Cho Cho, Yingwei Hu, Yuping Zhang, Chandan Kumar-Sinha, Weiping Ma, Anna Calinawan, Matthew A. Wyczalkowski, Michael C. Wendl, Yuefan Wang, Shenghao Guo, Cissy Zhang, Anne Le, Aniket Dagar, Alex Hopkins, Hanbyul Cho, Felipe da Veiga Leprevost, Xiaojun Jing, Guo Ci Teo, Wenke Liu, Melissa A. Reimers, Russell Pachynski, Alexander J. Lazar, Arul M. Chinnaiyan, Brian A. Van Tine, Bing Zhang, Karin D. Rodland, Gad Getz, D. R. Mani, Pei Wang, Feng Chen, Galen Hostetter, Mathangi Thiagarajan, W. Marston Linehan, David Fenyo, Scott D. Jewell, Gilbert S. Omenn, Rohit Mehra, Maciej Wiznerowicz, Ana I. Robles, Mehdi Mesri, Tara Hiltke, Eunkyung An, Henry Rodriguez, Daniel W. Chan, Christopher J. Ricketts, Alexey I. Nesvizhskii, Hui Zhang, Li Ding
Summary: By integrating histopathologic, proteogenomic, and metabolomic analyses, this study reveals the inter- and intratumoral heterogeneity of clear cell renal cell carcinomas (ccRCCs). It identifies high-risk disease subsets based on tumor grade, BAP1 mutation, genome instability, hypermethylation, and protein glycosylation signature. RNA sequencing provides insights into gene signatures and potential targeted therapies, while in vitro cell line studies validate the efficacy of inhibiting identified phosphoproteome targets.
Article
Biochemical Research Methods
Daniel A. Polasky, Daniel J. Geiszler, Fengchao Yu, Kai Li, Guo Ci Teo, Alexey I. Nesvizhskii
Summary: Posttranslational modifications of proteins play crucial roles in defining and regulating protein functions. Traditional methods for identifying these modifications using mass spectrometry-based proteomics have limitations, as they treat modifications as static attachments to peptide sequences. However, many modifications undergo fragmentation during mass spectrometry experiments, offering opportunities for improved searches. In this study, a new labile mode in the MSFragger search engine was developed to incorporate modification-specific fragment ions, resulting in significant improvements in identifying phosphopeptides, RNA-crosslinked peptides, and ADP-ribosylated peptides.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Multidisciplinary Sciences
Georges Bedran, Daniel A. Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier A. Alfaro, Marcin Cieslik, Alexey I. Nesvizhskii
Summary: In this study, a fast computational workflow merging the MSFragger-Glyco search algorithm with a false discovery rate control is introduced for analyzing glycopeptides from mass spectrometry-based immunopeptidome data. The authors analyze eight large-scale publicly available studies and find that glycosylated MHC-associated peptides are predominantly presented by MHC class II. They present a comprehensive resource, HLA-Glyco, which contains over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides from 1,049 distinct protein glycosylation sites. This resource provides valuable insights into glycosylation properties in antigen recognition and immune modulation.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Carolina Rojas Ramirez, Jessica A. Espino, Lisa M. Jones, Daniel A. Polasky, Alexey I. Nesvizhskii
Summary: Monitoring protein structure before and after environmental alterations can provide insights into protein function. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry allows for monitoring of structural rearrangements by exposing proteins to radicals. However, the challenges of processing FPOP data have limited its proteome-scale uses. In this study, a computational workflow was developed to analyze FPOP data sets more efficiently, enabling the identification of modified peptide spectra at a faster rate than previous methods.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Hana Popelka, Vikramjit Lahiri, Wayne D. Hawkins, Felipe da Veiga Leprevost, Alexey I. Nesvizhskii, Daniel J. Klionsky
Summary: The intrinsically disordered protein region (IDPR) of Atg12 protein plays an important role in its functional structure, as it is positioned in proximity to the ubiquitin-like (UBL) domain. Deletion in IDPR disrupts the integrity of the UBL domain, while a mutation in the predicted α0 helix in IDPR prevents Atg12 from binding to Atg7 and Atg10, impacting its function in the ubiquitin-like conjugation cascade.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Vi T. Tang, Prabhodh S. Abbineni, Felipe da Veiga Leprevost, Venkatesha Basrur, Rami Khoriaty, Brian T. Emmer, Alexey I. Nesvizhskii, David Ginsburg
Summary: Proteins are transported to the Golgi apparatus through COPII-coated vesicles or tubules, with LMAN1 and SURF4 being important receptors in this process. LMAN1 has limited clients in HuH7 cells, while SURF4 traffics a broad range of cargoes, suggesting complex cargo recognition mechanisms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Fengchao Yu, Guo Ci Teo, Andy T. T. Kong, Klemens Froehlich, Ginny Xiaohe Li, Vadim Demichev, Alexey I. Nesvizhskii
Summary: MSFragger-DIA is a fast and sensitive tool for direct peptide identification from DIA spectra, demonstrating excellent performance in applications such as large-scale tumor studies and single-cell proteomics.
NATURE COMMUNICATIONS
(2023)
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
Multidisciplinary Sciences
Daniel J. Geiszler, Daniel A. Polasky, Fengchao Yu, Alexey I. Nesvizhskii
Summary: Post-translational modifications are important in proteomics, but can complicate searches for modified peptides. The authors present an automated method to find diagnostic spectral features for any modification, improving peptide recovery and localization. They demonstrate the utility of this approach for various modifications and analyze the interactions between ion intensity and statistical properties. This method has been incorporated into PTM-Shepherd and FragPipe.
NATURE COMMUNICATIONS
(2023)
Review
Multidisciplinary Sciences
Ieva Bagdonaite, Stacy A. Malaker, Daniel A. Polasky, Nicholas M. Riley, Katrine Schjoldager, Sergey Y. Vakhrushev, Adnan Halim, Kiyoko F. Aoki-Kinoshita, Alexey I. Nesvizhskii, Carolyn R. Bertozzi, Hans H. Wandall, Benjamin L. Parker, Morten Thaysen-Andersen, Nichollas E. Scott
Summary: This Primer provides an overview of glycoproteomic methods and their applications, including glycopeptide analysis, sample selection, and mass spectrometry techniques. It focuses on the study of N-linked and O-linked glycosylation and provides insights into future directions in the field.
NATURE REVIEWS METHODS PRIMERS
(2022)