Suresh Poudel, Zuo-Fei Yuan, Yingxue Fu, Long Wu, Him Shrestha, Anthony A High, Junmin Peng, Xusheng Wang
{"title":"JUMPlib: Integrative Search Tool Combining Fragment Ion Indexing with Comprehensive TMT Spectral Libraries.","authors":"Suresh Poudel, Zuo-Fei Yuan, Yingxue Fu, Long Wu, Him Shrestha, Anthony A High, Junmin Peng, Xusheng Wang","doi":"10.1021/acs.jproteome.4c00410","DOIUrl":"10.1021/acs.jproteome.4c00410","url":null,"abstract":"<p><p>The identification of peptides is a cornerstone of mass spectrometry-based proteomics. Spectral library-based algorithms are well-established methods to enhance the identification efficiency of peptides during database searches in proteomics. However, these algorithms are not specifically tailored for tandem mass tag (TMT)-based proteomics due to the lack of high-quality TMT spectral libraries. Here, we introduce JUMPlib, a computational tool for a TMT-based spectral library search. JUMPlib comprises components for generating spectral libraries, conducting library searches, filtering peptide identifications, and quantifying peptides and proteins. Fragment ion indexing in the libraries increases the search speed and utilizing the experimental retention time of precursor ions improves peptide identification. We found that methionine oxidation is a major factor contributing to large shifts in peptide retention time. To test the JUMPlib program, we curated two comprehensive human libraries for the labeling of TMT6/10/11 and TMT16/18 reagents, with ∼286,000 precursor ions and ∼304,000 precursor ions, respectively. Our analyses demonstrate that JUMPlib, employing the fragment ion index strategy, enhances search speed and exhibits high sensitivity and specificity, achieving approximately a 25% increase in peptide-spectrum matches compared to other search tools. Overall, JUMPlib serves as a streamlined computational platform designed to enhance peptide identification in TMT-based proteomics. Both the JUMPlib source code and libraries are publicly available.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"410-418"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142880694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Veronica Ghini, Ana Isabel Tristán, Giorgio Di Paco, Lara Massai, Michele Mannelli, Tania Gamberi, Ignacio Fernández, Antonio Rosato, Paola Turano, Luigi Messori
{"title":"Novel NMR-Based Approach to Reveal the 'Metabolic Fingerprint' of Cytotoxic Gold Drugs in Cancer Cells.","authors":"Veronica Ghini, Ana Isabel Tristán, Giorgio Di Paco, Lara Massai, Michele Mannelli, Tania Gamberi, Ignacio Fernández, Antonio Rosato, Paola Turano, Luigi Messori","doi":"10.1021/acs.jproteome.4c00904","DOIUrl":"10.1021/acs.jproteome.4c00904","url":null,"abstract":"<p><p>A combination of pathway enrichment and metabolite clustering analysis is used to interpret untargeted <sup>1</sup>H NMR metabolomics data, enabling a biochemically informative comparison of the effects induced by a panel of known cytotoxic gold(I) and gold(III) compounds in A2780 ovarian cancer cells. The identification of the most dysregulated pathways for the major classes of compounds highlights specific chemical features that lead to common biological effects. The proposed approach may have broader applicability to the screening of metal-based drug candidate libraries, which is always complicated by their multitarget nature, and support the comprehensive interpretation of their metabolic actions.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"813-823"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samuel A Krug, Saba Shahzad, William T Witt, Mariette Barbier, Angela Wilks, Maureen A Kane
{"title":"Quantitative LC-MS/MS Analysis of Endogenous <i>Pseudomonas aeruginosa</i> Isomeric Metabolites Biliverdin IX Alpha, Beta, and Delta in Cell Culture Supernatant, Cell Pellet, and Lung Tissue.","authors":"Samuel A Krug, Saba Shahzad, William T Witt, Mariette Barbier, Angela Wilks, Maureen A Kane","doi":"10.1021/acs.jproteome.4c00750","DOIUrl":"10.1021/acs.jproteome.4c00750","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> (<i>Pa</i>) utilizes heme as an iron source from the host during infection. Biliverdin beta and delta (BVIXβ and BVIXδ) are generated by HemO, specific to <i>Pa</i>, while biliverdin alpha is generated from the bacterial BphO system and by mammalian heme oxygenases. Here, we have developed and characterized a quantitative LC-MS/MS assay for the separation of three endogenous isomers, BVIXα, BVIXβ, and BVIXδ. The assay was validated for accuracy, precision, linearity, extraction recovery, solution stability, freeze-thaw stability, benchtop stability, postextraction stability, and nonspecific oxidation of BVIX. The addition of an antioxidant, butylated hydroxytoluene, during sample preparation is needed in order to prevent coupled oxidation from inflating quantitative values of BVIX. The assay development included optimization of a liquid-liquid extraction for bacterial culture supernatants and sample preparation procedures for cell pellets and tissue homogenate to reduce sample demand and automate the extraction procedure in a 96-well format, to enhance extraction throughput. This method was applied to analyze isomer distribution in <i>Pa</i> supernatant, bacterial pellet, and infected lung tissue from <i>Pa</i>-challenged mice. This method can be used in the future for low-volume culture samples, as well as tissue samples, to understand the mechanisms of virulence and inform future drug development.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"649-656"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tibo Vande Moortele, Bram Devlaminck, Simon Van de Vyver, Tim Van Den Bossche, Lennart Martens, Peter Dawyndt, Bart Mesuere, Pieter Verschaffelt
{"title":"Unipept in 2024: Expanding Metaproteomics Analysis with Support for Missed Cleavages and Semitryptic and Nontryptic Peptides.","authors":"Tibo Vande Moortele, Bram Devlaminck, Simon Van de Vyver, Tim Van Den Bossche, Lennart Martens, Peter Dawyndt, Bart Mesuere, Pieter Verschaffelt","doi":"10.1021/acs.jproteome.4c00848","DOIUrl":"10.1021/acs.jproteome.4c00848","url":null,"abstract":"<p><p>Unipept, a pioneering software tool in metaproteomics, has significantly advanced the analysis of complex ecosystems by facilitating both taxonomic and functional insights from environmental samples. From the onset, Unipept's capabilities focused on tryptic peptides, utilizing the predictability and consistency of trypsin digestion to efficiently construct a protein reference database. However, the evolving landscape of proteomics and emerging fields like immunopeptidomics necessitate a more versatile approach that extends beyond the analysis of tryptic peptides. In this article, we present a significant update to the underlying index structure of Unipept, which is now powered by a Sparse Suffix Array index. This advancement enables the analysis of semitryptic peptides, peptides with missed cleavages, and nontryptic peptides such as those encountered in other research fields such as immunopeptidomics (e.g., MHC- and HLA-peptides). This new index benefits all tools in the Unipept ecosystem such as the web application, desktop tool, application programming interface (API), and command line interface. A benchmark study highlights significantly improved performance in handling missed cleavages, preserving the same level of accuracy.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"949-954"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
David J Degnan, Daniel M Claborne, Rachel E Richardson, Clayton W Strauch, Evan C Glasscock, Dusan Veličković, Kristin E Burnum-Johnson, Bobbie-Jo M Webb-Robertson, Kelly G Stratton, Lisa M Bramer
{"title":"MODE: A Web Application for Interactive Visualization and Exploration of Omics Data.","authors":"David J Degnan, Daniel M Claborne, Rachel E Richardson, Clayton W Strauch, Evan C Glasscock, Dusan Veličković, Kristin E Burnum-Johnson, Bobbie-Jo M Webb-Robertson, Kelly G Stratton, Lisa M Bramer","doi":"10.1021/acs.jproteome.4c00650","DOIUrl":"10.1021/acs.jproteome.4c00650","url":null,"abstract":"<p><p>Studies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as \"omics\") data allow researchers to find biomarkers or molecular targets or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data are multidimensional, and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries do not allow exploration of detailed patterns in omics data that may have biological relevance. The use of interactive HTML displays with plots allows researchers to interact with omics data at a detailed level, but building these displays requires significant coding expertise. To overcome this barrier, the software MODE was built to empower users to build their own interactive HTML displays to support scientific discovery. These displays are easily shareable, do not depend on a specific operating system, and allow users to sort and filter plots by categorical or numerical variables called metas. MODE allows users to build and share these displays with several options for plot design and meta selection. The MODE web application and its capabilities are presented and then demonstrated on lipidomics data from a leaf wounding study.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"911-918"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hyun-Kyung Woo, Hee-Sung Ahn, Juhee Park, Jonghoon Bae, Bokyung Kim, Jiyoung Yu, Jeong Kon Seo, Kyunggon Kim, Yoon-Kyoung Cho
{"title":"Size-Dependent Separation of Extracellular Vesicle Subtypes with Exodisc Enabling Proteomic Analysis in Prostate Cancer.","authors":"Hyun-Kyung Woo, Hee-Sung Ahn, Juhee Park, Jonghoon Bae, Bokyung Kim, Jiyoung Yu, Jeong Kon Seo, Kyunggon Kim, Yoon-Kyoung Cho","doi":"10.1021/acs.jproteome.4c00945","DOIUrl":"10.1021/acs.jproteome.4c00945","url":null,"abstract":"<p><p>Extracellular vesicles (EVs) are emerging as crucial biomarkers in cancer diagnostics and therapeutics with their heterogeneity presenting both challenges and opportunities in prostate cancer research. However, existing methods for isolating and characterizing EV subtypes have been limited by inefficient separation and inadequate proteomic analysis. Here we show an optimized centrifugal microfluidic device, Exodisc, that efficiently isolates large quantities of EV subtypes from particle-enriched medium, enabling comprehensive proteomic analysis of small (EV-S, 20-200 nm) and large (EV-L, >200 nm) EVs. Using this device, we successfully separated EV-S and EV-L from prostate cancer cell lines LNCaP and PC3. Mass spectrometry-based proteomics revealed that EV proteins reflect parental cell characteristics more than EV size, with EV-L demonstrating increased expression of PSMA-correlated proteins. Our optimized protocol addresses challenges in EV isolation and characterization, providing a more effective method for studying cellular and molecular mechanisms of specific EV subtypes. This study extends the potential use of EVs as a liquid biopsy for cancer theranostics, paving the way for more precise isolation of EV subtypes and potentially leading to improved biomarker discovery and the development of personalized treatments.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"861-870"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shaohua Zhan, Yan Yang, Shuwei Deng, Xinnan Liu, Liyan Cui, Tianxiao Wang
{"title":"The Ubiquitin Ligase CHIP Accelerates Papillary Thyroid Carcinoma Metastasis via the Transgelin-Matrix Metalloproteinase-9 Axis.","authors":"Shaohua Zhan, Yan Yang, Shuwei Deng, Xinnan Liu, Liyan Cui, Tianxiao Wang","doi":"10.1021/acs.jproteome.4c00726","DOIUrl":"10.1021/acs.jproteome.4c00726","url":null,"abstract":"<p><p>The carboxyl-terminus of Hsp70-interacting protein (CHIP) plays crucial roles in tumorigenesis and immunity, with previous studies suggesting a double-edged sword in thyroid cancer. However, its precise functions and underlying molecular mechanisms in thyroid cancer remained unclear. Here, we demonstrate through immunohistochemistry (IHC) that CHIP expression progressively increases from normal thyroid tissue to primary papillary thyroid carcinoma (PTC) and lymph node metastases, with CHIP levels positively correlating with lymph node metastasis (<i>P</i> = 0.006). Moreover, CHIP overexpression enhanced thyroid cancer cell migration and invasion without significantly affecting cell viability. Tandem mass tag (TMT)-based LC-MS/MS analysis revealed that CHIP-regulated differentially expressed proteins, notably transgelin, were predominantly associated with metastasis-related pathways. Western blot, qPCR, and TCGA-THCA cohort data confirmed that CHIP regulates transgelin expression at the protein but not the genetic level. Mechanistically, CHIP promotes extracellular matrix degradation through the transgelin-matrix metalloproteinase-9 (MMP-9) axis, thereby facilitating PTC progression. Collectively, our findings indicate that CHIP expression was closely related to the progression and metastasis of PTC, suggesting that CHIP functions as a novel tumor oncoprotein in PTC via the transgelin-MMP-9 signaling axis.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"589-598"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marina Álvaro-Moya, Alba Blesa, Daniel Prieto, Elvira Román, Jesús Pla, Rebeca Alonso-Monge
{"title":"Identification of <i>Candida albicans</i> Antigens Recognized by Murine Intestinal IgAs by a Gel-Independent Immunoproteomic Approach.","authors":"Marina Álvaro-Moya, Alba Blesa, Daniel Prieto, Elvira Román, Jesús Pla, Rebeca Alonso-Monge","doi":"10.1021/acs.jproteome.4c00691","DOIUrl":"10.1021/acs.jproteome.4c00691","url":null,"abstract":"<p><p>As part of the intestinal microbiota, <i>Candida albicans</i> can elicit a humoral response in the gastrointestinal tract (GIT) that is mainly directed toward hyphal antigens. This response has been implicated in controlling the invasive form of the fungus and maintaining the yeast as an innocuous commensal. However, the specific targets of this response are still unknown. Here, we used a gel-free immunoproteomic methodology to identify <i>C. albicans</i> gut immunogens. For this goal, we previously obtained specific secreted IgA from mice colonized with <i>C. albicans</i>. Then, secretome and surfome from <i>C. albicans</i> wild-type filaments were obtained and incubated with magnetic beads linked to antimouse IgA antibodies. sIgA targets were immunoprecipitated and analyzed by mass spectrometry. A third sample bearing the <i>C. albicans</i> antigen-sIgA complex was also examined. Those identified proteins that exhibited a higher percentile of relative abundance were considered for further analysis. From those, 35 proteins coincided among the three samples. Remarkably, about 40% of the identified proteins appeared in the databases as uncharacterized. The results were then validated by immunofluorescence assays overexpressing some of the genes identified in a yeast-lock <i>C. albicans</i> mutant. Adhesins such as Als3, Als1, and Hwp1 were corroborated to be IgA targets, as well as the chaperone Ssa2. Therefore, this gel-free immunoproteomic approach has been useful to identify new <i>C. albicans</i> antigens that generate a specific humoral response in the murine gut.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"657-671"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Naman Kharbanda, Ankit Biswas, Arundhati Tiwari, Pragya Tailor, Sandhini Saha, Nitya Wadhwa, Ramachandran Thiruvengadam, Dinakar M Salunke, Shinjini Bhatnagar, Garbh-Ini Study Group, Pallavi Kshetrapal, Tushar Kanti Maiti
{"title":"Placental Proteomics Reveals an Elevated Level of Aldo-Keto Reductase 1-B1, Highlighting Its Potential Role in Spontaneous Preterm Birth.","authors":"Naman Kharbanda, Ankit Biswas, Arundhati Tiwari, Pragya Tailor, Sandhini Saha, Nitya Wadhwa, Ramachandran Thiruvengadam, Dinakar M Salunke, Shinjini Bhatnagar, Garbh-Ini Study Group, Pallavi Kshetrapal, Tushar Kanti Maiti","doi":"10.1021/acs.jproteome.4c00698","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00698","url":null,"abstract":"<p><p>Preterm birth (PTB) refers to the delivery of a baby before the completion of 37 weeks of gestation. It is a significant global health issue with implications for both mothers and neonates. The placenta is a transient organ crucial in the sustenance of pregnancy until parturition; its dysfunction is associated with different adverse pregnancy outcomes, including PTB. We conducted a nested case-control study of 40 placental tissue samples from preterm and term deliveries to study their comparative protein profiles. Label-free quantitation (LFQ) revealed 23 differentially expressed proteins (DEPs). Aldo-keto reductase-B1 (AKR1B1) protein expression profile exhibited a declining trajectory with an increasing period of gestation (POG). Immunoblotting and immunohistochemistry analyses of placental samples also revealed elevated protein levels in extreme preterm samples. AKR1B1 is a functional Prostaglandin F synthase responsible for the synthesis of Prostaglandin-F2α, a prostanoid that is elevated during parturition and involved in cervical ripening, membrane rupture, myometrial contraction, and inflammation. Hence, our finding supports the idea that elevated AKR1B1 levels play a significant role in the pathology of preterm birth by amplifying Prostaglandin-F2α synthesis in the placental milieu and can be further explored as a potential predictor of this condition. Data are available via ProteomeXchange with the identifier PXD043480.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 2","pages":"612-623"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of Proteome ResearchPub Date : 2025-02-07DOI: 10.1021/acs.jproteome.4c0109810.1021/acs.jproteome.4c01098
Brian C. Searle*, Blandine Chazarin, Ben C. Collins, Deepti J. Kundu, Shixia Huang, Qingsong Lin, Yansheng Liu, Teck Yew Low, Julian Saba, Tiannan Guo, Giuseppe Palmisano and Justyna Fert-Bober,
{"title":"Advancing Scientific Communication in Proteomics","authors":"Brian C. Searle*, Blandine Chazarin, Ben C. Collins, Deepti J. Kundu, Shixia Huang, Qingsong Lin, Yansheng Liu, Teck Yew Low, Julian Saba, Tiannan Guo, Giuseppe Palmisano and Justyna Fert-Bober, ","doi":"10.1021/acs.jproteome.4c0109810.1021/acs.jproteome.4c01098","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01098https://doi.org/10.1021/acs.jproteome.4c01098","url":null,"abstract":"","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 2","pages":"381–382 381–382"},"PeriodicalIF":3.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}