Journal of Proteome Research最新文献_第9页

In-Depth Proteomic Analysis of Tissue Interstitial Fluid Reveals Biomarker Candidates Related to Varying Differentiation Statuses in Gastric Adenocarcinoma.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-06 DOI: 10.1021/acs.jproteome.4c01067

Juxiang Zhang, An Xiong, Yuanyuan Yang, Yiou Cao, Mengxuan Yang, Chang Su, Ming Lei, Yi Chen, Xiaodong Shen, Puhua Wang, Chencheng Shi, Rongjian Zhou, Ning Ren, Hongwen Zhu, Chunyan Yuan, Shaoqun Liu, Fei Teng

{"title":"In-Depth Proteomic Analysis of Tissue Interstitial Fluid Reveals Biomarker Candidates Related to Varying Differentiation Statuses in Gastric Adenocarcinoma.","authors":"Juxiang Zhang, An Xiong, Yuanyuan Yang, Yiou Cao, Mengxuan Yang, Chang Su, Ming Lei, Yi Chen, Xiaodong Shen, Puhua Wang, Chencheng Shi, Rongjian Zhou, Ning Ren, Hongwen Zhu, Chunyan Yuan, Shaoqun Liu, Fei Teng","doi":"10.1021/acs.jproteome.4c01067","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01067","url":null,"abstract":"The proteomic heterogeneity of gastric adenocarcinoma (GC) has been extensively investigated at the bulk tissue level, which can only provide an average molecular state. In this study, we collected an in-depth quantitative proteomic dataset of tissues and interstitial fluids (ISFs) from both poorly and non-poorly differentiated GC and presented a comprehensive analysis from several perspectives. Comparison of proteomes between ISFs and tissues revealed that ISF exhibited higher abundances of proteins associated with blood microparticles, protein-lipid complexes, immunoglobulin complexes, and high-density lipoprotein particles. Also, consistent and inconsistent protein abundance changes between them were revealed by a correlation analysis. Interestingly, a more pronounced difference between tumors and normal adjacent tissues was found at the ISF level, which accurately reflected tissue properties compared to those of bulk tissue. Two ISF-derived biomarker candidates, calsyntenin-1 (CLSTN1) and prosaposin (PSAP), were identified by distinguishing patients with different differentiation statuses and were further validated in serum samples. Additionally, the silencing of CLSTN1 and PSAP was demonstrated to suppress cell proliferation, migration, and invasion in poorly differentiated gastric cancer cell lines. In summary, the ISF proteome offers a new perspective on tumor biology. This study provides a valuable resource that significantly enhances the understanding of GC and may ultimately benefit clinical practice.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254145","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}

引用次数: 0

PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-05 DOI: 10.1021/acs.jproteome.4c00743

Dominik Madej, Henry Lam

{"title":"PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.","authors":"Dominik Madej, Henry Lam","doi":"10.1021/acs.jproteome.4c00743","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00743","url":null,"abstract":"Validating false discovery rate (FDR) estimation is an essential but surprisingly understudied aspect of method development in shotgun proteomics. Currently available validation protocols mostly rely on ground truth data sets, which typically involve manipulating the properties of the search space or query spectra used. As a result, comparing estimated FDR and ground truth-based false discovery proportion values may not be representative of the scenarios involving natural data sets encountered in practice. In this study, we introduce PyViscount─a Python tool implementing a novel validation protocol based on random search space partition, which enables generating a quasi ground-truth using unaltered search spaces of unique candidate peptides and generic data sets of experimental query spectra. Furthermore, validation of existing FDR estimation methods by PyViscount is consistent with alternative validation protocols. The presented novel approach to validation free from the need for synthetic data sets or dubious manipulation of the data may be an attractive alternative for proteomics practitioners, allowing them to obtain deeper insights into the performance of existing and new FDR estimation methods.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187765","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}

引用次数: 0

Unraveling the Impact of TLR4 and Sex on Chronic Alcohol Consumption-Induced Lipidome Dysregulation in Extracellular Vesicles.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-05 DOI: 10.1021/acs.jproteome.4c00786

Carla Perpiñá-Clérigues, Susana Mellado, Cristina Galiana-Roselló, Francisco García-García, María Pascual

{"title":"Unraveling the Impact of TLR4 and Sex on Chronic Alcohol Consumption-Induced Lipidome Dysregulation in Extracellular Vesicles.","authors":"Carla Perpiñá-Clérigues, Susana Mellado, Cristina Galiana-Roselló, Francisco García-García, María Pascual","doi":"10.1021/acs.jproteome.4c00786","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00786","url":null,"abstract":"The lipids that form extracellular vesicles (EVs) play critical structural and regulatory roles, and cutting-edge bioinformatics strategies have shown the ability to decipher lipid metabolism and related molecular mechanisms. We previously demonstrated that alcohol abuse induces an inflammatory immune response through Toll-like receptor 4 (TLR4), leading to structural and cognitive dysfunction. This study evaluated how TLR4 and sex as variables (male/female) impact the lipidome of plasma-resident EVs after chronic alcohol exposure. Using a mouse model of chronic ethanol exposure in wild-type and TLR4-deficient mice, enrichment networks generated by LINEX2 highlighted significant ethanol-induced changes in the EV lipid substrate-product of enzyme reactions associated with glycerophospholipid metabolism. We also demonstrated ethanol-induced differences in Lipid Ontology enrichment analysis in EVs, focusing on terms related to lipid bilayer properties. A lipid abundance analysis revealed higher amounts of significant lipid subclasses in all experimental comparisons associated with inflammatory responses and EV biogenesis/secretion. These findings suggest that interrogating EV lipid abundance with a sensitive lipidomic-based strategy can provide deep insight into the molecular mechanisms underlying biological processes associated with sex, alcohol consumption, and TLR4 immune responses and open new avenues for biomarker identification and therapeutic development.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187512","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}

引用次数: 0

Serum N-Glycomics with Nano-LC-QToF LC-MS/MS Reveals N-Glycan Biomarkers for Glioblastoma, Meningioma, and High-Grade Meningioma.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-05 DOI: 10.1021/acs.jproteome.4c01090

Atit Silsirivanit, Michael Russelle S Alvarez, Sheryl Joyce Grijaldo-Alvarez, Riya Gogte, Amnat Kitkhuandee, Nontaphon Piyawattanametha, Wunchana Seubwai, Sukanya Luang, Orasa Panawan, Panupong Mahalapbutr, Kulthida Vaeteewoottacharn, Kanlayanee Sawanyawisuth, Worachart Let-Itthiporn, Charupong Saengboonmee, Pichayen Duangthongphon, Kritsakorn Jingjit, Anuchit Pankongsap, Sakda Waraasawapati, Chaiwat Aphivatanasiri, Carlito B Lebrilla

{"title":"Serum N-Glycomics with Nano-LC-QToF LC-MS/MS Reveals N-Glycan Biomarkers for Glioblastoma, Meningioma, and High-Grade Meningioma.","authors":"Atit Silsirivanit, Michael Russelle S Alvarez, Sheryl Joyce Grijaldo-Alvarez, Riya Gogte, Amnat Kitkhuandee, Nontaphon Piyawattanametha, Wunchana Seubwai, Sukanya Luang, Orasa Panawan, Panupong Mahalapbutr, Kulthida Vaeteewoottacharn, Kanlayanee Sawanyawisuth, Worachart Let-Itthiporn, Charupong Saengboonmee, Pichayen Duangthongphon, Kritsakorn Jingjit, Anuchit Pankongsap, Sakda Waraasawapati, Chaiwat Aphivatanasiri, Carlito B Lebrilla","doi":"10.1021/acs.jproteome.4c01090","DOIUrl":"10.1021/acs.jproteome.4c01090","url":null,"abstract":"Alteration of glycosylation in cancer cells leads to the expression of tumor-associated glycans, which can be used as biomarkers for diagnosis and prognostic prediction of diseases. In this study, we used nano-LC-QToF to identify serum N-glycan biomarkers for the detection of brain tumors. We observed an increase in sialylated N-glycans and a decrease in fucosylated N-glycans in the serum of patients with glioblastoma (GBM) and meningioma (MG) compared to healthy individuals. In GBM, a combination of increased serum sialylated N-glycan (6_4_0_2 compound) and decreased fucosylated N-glycan (4_4_1_0 compound) was identified as the most appropriate panel, with an area under the curve (AUC) of 0.8660, 78.95% sensitivity, 84.21% specificity, and 82.89% accuracy. For MG, a combination of decreased 6_6_2_0 and 5_5_2_0 compounds and increased 4_4_1_1 compound achieved an AUC of 0.9260, 82.35% sensitivity, 78.57% specificity, and 80.26% accuracy for diagnosis of MG. Additionally, an increase in 5_5_1_0 and 4_3_0_0 compounds combined with a decrease in 7_7_4_3 was associated with high-grade MG (WHO grades II-III). In conclusion, we identified serum N-glycan profiles associated with brain tumors, highlighting their potential as biomarkers for the diagnosis and prognosis of these diseases.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187504","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}

引用次数: 0

Searching for Sulfotyrosines (sY) in a HA(pY)STACK.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-05 DOI: 10.1021/acs.jproteome.4c00907

Jordan Tzvetkov, Claire E Eyers, Patrick A Eyers, Kerry A Ramsbottom, Sally O Oswald, John A Harris, Zhi Sun, Eric W Deutsch, Andrew R Jones

{"title":"Searching for Sulfotyrosines (sY) in a HA(pY)STACK.","authors":"Jordan Tzvetkov, Claire E Eyers, Patrick A Eyers, Kerry A Ramsbottom, Sally O Oswald, John A Harris, Zhi Sun, Eric W Deutsch, Andrew R Jones","doi":"10.1021/acs.jproteome.4c00907","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00907","url":null,"abstract":"Protein sulfation can be crucial in regulating protein-protein interactions but remains largely underexplored. Sulfation is nearly isobaric to phosphorylation, making it particularly challenging to investigate using mass spectrometry. The degree to which tyrosine sulfation (sY) is misidentified as phosphorylation (pY) is, thus, an unresolved concern. This study explores the extent of sY misidentification within the human phosphoproteome by distinguishing between sulfation and phosphorylation based on their mass difference. Using Gaussian mixture models (GMMs), we screened ∼45 M peptide-spectrum matches (PSMs) from the PeptideAtlas human phosphoproteome build for peptidoforms with mass error shifts indicative of sulfation. This analysis pinpointed 104 candidate sulfated peptidoforms, backed up by Gene Ontology (GO) terms and custom terms linked to sulfation. False positive filtering by manual annotation resulted in 31 convincing peptidoforms spanning 7 known and 7 novel sY sites. Y47 in calumenin was particularly intriguing since mass error shifts, acidic motif conservation, and MS2 neutral loss patterns characteristic of sulfation provided strong evidence that this site is sulfated rather than phosphorylated. Overall, although misidentification of sulfation in phosphoproteomics data sets derived from cell and tissue intracellular extracts can occur, it appears relatively rare and should not be considered a substantive confounding factor in high-quality phosphoproteomics data sets.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187493","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}

引用次数: 0

Query Mix-Max Method for FDR Estimation Supported by Entrapment Queries.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-05 DOI: 10.1021/acs.jproteome.4c00744

Dominik Madej, Henry Lam

{"title":"Query Mix-Max Method for FDR Estimation Supported by Entrapment Queries.","authors":"Dominik Madej, Henry Lam","doi":"10.1021/acs.jproteome.4c00744","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00744","url":null,"abstract":"Estimating the false discovery rate (FDR) is one of the key steps in ensuring appropriate error control in the analysis of shotgun proteomics data. Traditional estimation methods typically rely on decoy sequence databases or spectral libraries, which may not always provide satisfactory results due to limitations of decoy construction methods. This study introduces the query mix-max (QMM) method, a decoy-free alternative for FDR estimation in proteomics. The QMM framework builds upon the existing mix-max procedure but replaces decoy matches with entrapment queries to estimate the number of false positive discoveries. Through simulations and real data set analyses, the QMM method was demonstrated to provide reasonably accurate FDR estimation across various scenarios, particularly when smaller sample-to-entrapment spectra ratios were achieved. The QMM method tends to be conservatively biased, particularly at higher FDR values, which can ensure stringent FDR control. While flexible, the protocol's effectiveness may vary depending on the evolutionary distance between the sample and entrapment organisms. It also requires a sufficient number of entrapment queries to provide stable FDR estimates, especially for low FDR values. Despite these limitations, the QMM method is a promising alternative as one of the first query-based FDR estimation approaches in shotgun proteomics.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187810","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}

引用次数: 0

LC-MS/MS-Profiling of Human Serum Unveils Significant Increase in Neuroinflammation and Carcinogenesis Following Chronic Organophosphate Exposure.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-04 DOI: 10.1021/acs.jproteome.4c00995

Vishal Sandilya, Dina El-Gameel, Mojgan Atashi, Thu Nguyen, Mojibola Fowowe, Md Mostofa Al Amin Bhuiyan, Oluwatosin Daramola, Judith Nwaiwu, Noha A Hamdy, Maha Ghanem, Labiba K El-Khordagui, Salwa M Abdallah, Ahmed El-Yazbi, Yehia Mechref

{"title":"LC-MS/MS-Profiling of Human Serum Unveils Significant Increase in Neuroinflammation and Carcinogenesis Following Chronic Organophosphate Exposure.","authors":"Vishal Sandilya, Dina El-Gameel, Mojgan Atashi, Thu Nguyen, Mojibola Fowowe, Md Mostofa Al Amin Bhuiyan, Oluwatosin Daramola, Judith Nwaiwu, Noha A Hamdy, Maha Ghanem, Labiba K El-Khordagui, Salwa M Abdallah, Ahmed El-Yazbi, Yehia Mechref","doi":"10.1021/acs.jproteome.4c00995","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00995","url":null,"abstract":"The utilization of organophosphate pesticides (OPs) has escalated in response to the growing global food demand driven by a rapidly increasing population and the environmental disruptions caused by climate change. While acute exposure leads to cholinergic poisoning, chronic OP exposure has been linked to organ dysfunction, inflammation, and carcinogenesis. Serum samples from healthy individuals (n = 11), patients with acute OP exposure (n = 12), and those with chronic OP exposure (n = 31) were analyzed to discern the differentially expressed pathways after acute and chronic OP exposure. Differential expression analysis identified 132 proteins altered in chronic exposure vs control, 86 in acute exposure vs control, and 124 in chronic vs acute exposure. Pathway analysis revealed increased blood coagulation and reduced LXR/RXR activation and DCHR24 signaling in both acute and chronic exposures. Elevated levels of pro-inflammatory proteins, such as S100A8, VWF, and GPIBA, were observed, particularly in chronic exposure, highlighting significant inflammatory effects of OP exposure. These findings provide insights into the pathological mechanisms underlying chronic OP exposure and its contribution to inflammation and long-term health risks.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187744","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}

引用次数: 0

Deep, Unbiased, and Quantitative Mass Spectrometry-Based Plasma Proteome Analysis of Individual Responses to mRNA COVID-19 Vaccine.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-04 DOI: 10.1021/acs.jproteome.4c00909

Ting Huang, Alex Rosa Campos, Jian Wang, Alexey Stukalov, Ramón Díaz, Svetlana Maurya, Khatereh Motamedchaboki, Daniel Hornburg, Laura R Saciloto-de-Oliveira, Camila Innocente-Alves, Yohana P Calegari-Alves, Serafim Batzoglou, Walter O Beys-da-Silva, Lucélia Santi

{"title":"Deep, Unbiased, and Quantitative Mass Spectrometry-Based Plasma Proteome Analysis of Individual Responses to mRNA COVID-19 Vaccine.","authors":"Ting Huang, Alex Rosa Campos, Jian Wang, Alexey Stukalov, Ramón Díaz, Svetlana Maurya, Khatereh Motamedchaboki, Daniel Hornburg, Laura R Saciloto-de-Oliveira, Camila Innocente-Alves, Yohana P Calegari-Alves, Serafim Batzoglou, Walter O Beys-da-Silva, Lucélia Santi","doi":"10.1021/acs.jproteome.4c00909","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00909","url":null,"abstract":"Global campaign against COVID-19 have vaccinated a significant portion of the world population in recent years. Combating the COVID-19 pandemic with mRNA vaccines played a pivotal role in the global immunization effort. However, individual responses to a vaccine are diverse and lead to varying vaccination efficacy. Despite significant progress, a complete understanding of the molecular mechanisms driving the individual immune response to the COVID-19 vaccine remains elusive. To address this gap, we combined a novel nanoparticle-based proteomic workflow with tandem mass tag (TMT) labeling, to quantitatively assess the proteomic changes in a cohort of 12 volunteers following two doses of the Pfizer-BioNTech mRNA COVID-19 vaccine. This optimized protocol seamlessly integrates comprehensive proteome analysis with enhanced throughput by leveraging the enrichment of low-abundant plasma proteins by engineered nanoparticles. Our data demonstrate the ability of this workflow to quantify over 3,000 proteins, providing the deepest view into COVID-19 vaccine-related plasma proteome study. We identified 69 proteins with boosted responses post-second dose and 74 proteins differentially regulated between individuals who contracted COVID-19 despite vaccination and those who did not. These findings offer valuable insights into individual variability in response to vaccination, demonstrating the potential of personalized medicine approaches in vaccine development.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187731","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}

引用次数: 0

Formaldehyde Fixation Helps Preserve the Proteome State during Single-Cell Proteomics Sample Processing and Analysis.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-03 DOI: 10.1021/acs.jproteome.4c00656

Ilaria Piga, Claire Koenig, Maico Lechner, Pierre Sabatier, Jesper V Olsen

{"title":"Formaldehyde Fixation Helps Preserve the Proteome State during Single-Cell Proteomics Sample Processing and Analysis.","authors":"Ilaria Piga, Claire Koenig, Maico Lechner, Pierre Sabatier, Jesper V Olsen","doi":"10.1021/acs.jproteome.4c00656","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00656","url":null,"abstract":"Mass spectrometry-based single-cell proteomics (SCP) is gaining momentum but remains limited to a few laboratories due to the high costs and specialized expertise required. The ability to send samples to specialized core facilities would benefit nonspecialist laboratories and popularize SCP for biological applications. However, no methods have been tested in SCP to \"freeze\" the proteome state while maintaining cell integrity for transfer between laboratories or prolonged sorting using fluorescence-activated cell sorting (FACS). This study evaluates whether short-term formaldehyde (FA) fixation can maintain the cell states. We demonstrate that short-term FA fixation does not substantially affect protein recovery, even without heating and strong detergents, and maintains analytical depth compared with classical workflows. Fixation also preserves drug-induced specific perturbations of the protein abundance during cell sorting and sample preparation for SCP analysis. Our findings suggest that FA fixation can facilitate SCP by enabling sample shipping and prolonged sorting, potentially democratizing access to SCP technology and expanding its application in biological research, thereby accelerating discoveries in cell biology and personalized medicine.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143121843","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}

引用次数: 0

MARLOWE: An Untargeted Proteomics, Statistical Approach to Taxonomic Classification for Forensics.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-02-03 DOI: 10.1021/acs.jproteome.3c00477

Fanny Chu, Sarah C Jenson, Anthony S Barente, Natalie C Heller, Eric D Merkley, Kristin H Jarman

{"title":"MARLOWE: An Untargeted Proteomics, Statistical Approach to Taxonomic Classification for Forensics.","authors":"Fanny Chu, Sarah C Jenson, Anthony S Barente, Natalie C Heller, Eric D Merkley, Kristin H Jarman","doi":"10.1021/acs.jproteome.3c00477","DOIUrl":"10.1021/acs.jproteome.3c00477","url":null,"abstract":"General proteomics research for fundamental science typically addresses laboratory- or patient-derived samples of known origin and composition. However, in a few research areas, such as environmental proteomics, clinical identification of infectious organisms, archeology, art/cultural history, and forensics, attributing the origin of a protein-containing sample to the organisms that produced it is a central focus. A small number of groups have approached this problem and developed software tools for taxonomic characterization and/or identification using bottom-up proteomics. Most such tools identify peptides via database search, and many rely on organism-specific peptides as markers. Our group recently introduced MARLOWE, a software tool for taxonomic characterization of unknown samples based on de novo peptide identification and signal-erosion-resistant strong peptides, which are shared peptides distributed in a taxonomy-dependent manner. In the current work, we further characterize the utility of MARLOWE using publicly available proteomics data from forensically-relevant samples. MARLOWE characterizes samples based on their protein profile, and returns ranked organism lists of potential contributors and taxonomic scores based on shared strong peptides between organisms. Overall, the correct characterization rate ranges between 44 and 100%, depending on the sample type and data acquisition parameters (with lower numbers associated with lower-quality data sets). MARLOWE demonstrates successful characterization of true contributors and close relatives, and provides sufficient specificity to distinguish certain microbial species. MARLOWE demonstrates its ability to provide insight into potential taxonomic sources for a wide range of sample types without prior assumptions about sample contents. This approach can find utility in forensic science and also broadly in bioanalytical applications that utilize proteomics approaches for taxonomic characterization.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077951","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}

引用次数: 0