Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite

Journal of Proteome Research, Год журнала: 2023, Номер 22(2), С. 615 - 624

Опубликована: Янв. 17, 2023

The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet ProteinProphet, were published 20 years ago. current release provides a large complement of tools for spectrum processing, searching, search validation, abundance computation, protein inference, more. Many the include machine-learning modeling to extract most information from sets build robust statistical models compute probabilities that derived is correct. Here we present latest on many TPP how can be deployed various platforms personal Windows laptops Linux clusters expansive cloud computing environments. We describe tutorials use variety ways synergistic projects leverage TPP. conclude with plans continued

Язык: Английский

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Instrumentation at the Leading Edge of Proteomics

Analytical Chemistry, Год журнала: 2024, Номер 96(20), С. 7976 - 8010

Опубликована: Май 13, 2024

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTInstrumentation at the Leading Edge of ProteomicsTrenton M. Peters-ClarkeTrenton Peters-ClarkeDepartment Chemistry, University Wisconsin─Madison, Madison, Wisconsin 53706, United StatesDepartment Biomolecular StatesMore by Trenton Peters-ClarkeView Biographyhttps://orcid.org/0000-0002-9153-2525, Joshua J. CoonJoshua CoonDepartment StatesMorgridge Institute for Research, 53715, CoonView Biographyhttps://orcid.org/0000-0002-0004-8253, and Nicholas Riley*Nicholas RileyDepartment Washington, Seattle, Washington 98195, States*Email: [email protected]More RileyView Biographyhttps://orcid.org/0000-0002-1536-2966Cite this: Anal. Chem. 2024, 96, 20, 7976–8010Publication Date (Web):May 13, 2024Publication History Received6 October 2023Accepted19 April 2024Revised17 2024Published online13 May inissue 21 2024https://pubs.acs.org/doi/10.1021/acs.analchem.3c04497https://doi.org/10.1021/acs.analchem.3c04497review-articleACS PublicationsCopyright © 2024 American Chemical SocietyRequest reuse permissionsArticle Views2104Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are COUNTER-compliant sum full text article downloads since November 2008 (both PDF HTML) across all institutions individuals. These metrics regularly updated to reflect usage leading up last few days.Citations number other articles citing this article, calculated Crossref daily. Find more information about citation counts.The Altmetric Attention Score is a quantitative measure attention that research has received online. Clicking on donut icon will load page altmetric.com with additional details score social media presence given article. how calculated. Share Add toView InAdd Full Text ReferenceAdd Description ExportRISCitationCitation abstractCitation referencesMore Options onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Dissociation,Ions,Mass spectrometry,Peptides proteins,Proteomics Get e-Alerts

Язык: Английский

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Proteomics of human biological fluids for biomarker discoveries: technical advances and recent applications

Expert Review of Proteomics, Год журнала: 2022, Номер 19(2), С. 131 - 151

Опубликована: Фев. 1, 2022

Biological fluids are routine samples for diagnostic testing and monitoring. Blood typically measured because of their moderate invasive collection high information content on health disease. Several body fluids, such as cerebrospinal fluid (CSF), also studied suited to specific pathologies. Over the last two decades, proteomics has quested identify protein biomarkers but with limited success. Recent technologies refined pipelines have accelerated profiling human biological fluids.We review proteomic identification biomarkers. These based antibodies/aptamers arrays or mass spectrometry (MS), new ones emerging. Advances in scalability throughput allowed better design studies cope sample size that until now prevailed due technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, milk proteomes been further profiled; we provide a non-exhaustive picture some recent highlights (mainly covering literature from 5 years Scopus database) using MS-based proteomics.While shadow genomics years, tools methodologies reached certain maturity. They discover innovative robust biofluid

Язык: Английский

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The complexity of kidney disease and diagnosing it – cystatin C, selective glomerular hypofiltration syndromes and proteome regulation

Journal of Internal Medicine, Год журнала: 2022, Номер 293(3), С. 293 - 308

Опубликована: Ноя. 17, 2022

Estimation of kidney function is often part daily clinical practice, mostly done by using the endogenous glomerular filtration rate (GFR)-markers creatinine or cystatin C. A recommendation to use both markers in parallel 2010 has resulted new knowledge concerning pathophysiology disorders identification a set disorders, selective hypofiltration syndromes. These syndromes, connected strong increases mortality and morbidity, are characterized reduction 5-30 kDa molecules, such as C, compared small molecules <1 dominating filtrate, for example water, urea creatinine. At least two types shrunken elongated pore syndrome, possible according model filtration. Selective syndromes prevalent investigated populations, patients with these display normal measured GFR creatinine-based GFR-estimates. The proteomic changes promoting development atherosclerosis, indicating antibodies specific receptor-blocking substances treatment modalities. Presently, KDIGO guidelines diagnosing do not recommend C general marker will therefore allow considerable number Furthermore, uninfluenced muscle mass, diet variations tubular secretion C-based GFR-estimation equations require controversial race sex terms, it obvious that should be future guidelines.

Язык: Английский

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The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Journal of Proteome Research, Год журнала: 2022, Номер 22(4), С. 1024 - 1042

Опубликована: Ноя. 1, 2022

The 2022 Metrics of the Human Proteome from HUPO Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) 19 750 predicted proteins coded in human genome, a net gain 50 since 2021 data sets generated around world and reanalyzed by HPP. Conversely, number neXtProt PE2, PE3, PE4 missing reduced 78 1421 to 1343. This represents continuing experimental progress on proteome parts list across all chromosomes, as well significant reclassifications. Meanwhile, applying proteomics vast array biological clinical studies continues yield findings growing integration with other omics platforms. We present highlights Chromosome-Centric HPP, Biology Disease-driven HPP Resource Pillars, compare features mass spectrometry Olink Somalogic platforms, note emergence translation products ribosome profiling small open reading frames, discuss launch initial Grand Challenge Project, "A Function Each Protein".

Язык: Английский

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Clinical applications of plasma proteomics and peptidomics: Towards precision medicine

PROTEOMICS - CLINICAL APPLICATIONS, Год журнала: 2022, Номер 16(6)

Опубликована: Май 1, 2022

In the context of precision medicine, disease treatment requires individualized strategies based on underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential develop new biomarkers diagnose, stratify, or possibly prevent diseases. Plasma an available source that greatly reflects physiological and pathological conditions body. An increasing number studies are focusing proteins peptides, including many involving Human Proteome Project (HPP) Organization (HUPO), proteomics peptidomics techniques emerging as critical tools for developing novel medicine preventative measures. Excitingly, plasma toolbox exhibits a huge potential studying pathogenesis diseases (e.g., COVID-19 cancer), identifying valuable improving clinical management. However, enormous complexity wide dynamic range makes proteome profiling challenging. Herein, we summarize recent advances in with focus their roles cancer research, aiming emphasize significance applications medicine.

Язык: Английский

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Autologous Platelet and Extracellular Vesicle-Rich Plasma as Therapeutic Fluid: A Review

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(4), С. 3420 - 3420

Опубликована: Фев. 8, 2023

The preparation of autologous platelet and extracellular vesicle-rich plasma (PVRP) has been explored in many medical fields with the aim to benefit from its healing potential. In parallel, efforts are being invested understand function dynamics PVRP that is complex composition interactions. Some clinical evidence reveals beneficial effects PVRP, while some report there were no effects. To optimize methods, functions mechanisms constituents should be better understood. With intention promote further studies therapeutic we performed a review on topics regarding composition, harvesting, assessment preservation, also experience following application humans animals. Besides acknowledged actions platelets, leukocytes different molecules, focus vesicles found abundant PVRP.

Язык: Английский

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Vago-splenic signal transduction of cardioprotection in humans

European Heart Journal, Год журнала: 2024, Номер 45(34), С. 3164 - 3177

Опубликована: Июнь 6, 2024

Abstract Background and Aims The spleen serves as an important relay organ that releases cardioprotective factor(s) upon vagal activation during remote ischaemic conditioning (RIC) in rats pigs. translation of these findings to humans was attempted. Methods Remote or electrical auricular tragus stimulation (ATS) were performed 10 healthy young volunteers, volunteers with splenectomy, 20 matched controls. Venous blood samples taken before after RIC/ATS placebo, a plasma dialysate infused into isolated perfused rat hearts subjected global ischaemia/reperfusion. Results Neither left nor right RIC ATS altered heart rate variability the study cohorts. With prepared ATS, respectively, infarct size (% ventricular mass) recipient 36 ± 6% (left RIC), 34 3% (right RIC) 31 5% ATS), 35 decreased from 4% 23 19 26 9% ATS); still reduced 4 days 9 RIC. In subgroup six such reduction abrogated by intravenous atropine. Infarct also but not their Conclusions humans, innervation are decisive for signal transduction ATS.

Язык: Английский

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π-HuB: the proteomic navigator of the human body

Nature, Год журнала: 2024, Номер 636(8042), С. 322 - 331

Опубликована: Дек. 11, 2024

Язык: Английский

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Proteomic patterns associated with ketamine response in major depressive disorders

Cell Biology and Toxicology, Год журнала: 2025, Номер 41(1)

Опубликована: Янв. 10, 2025

Major depressive disorder (MDD) is characterized by persistent feelings of sadness and loss interest. Ketamine has been widely used to treat MDD owing its rapid effect in relieving symptoms. Importantly, not all patients respond ketamine treatment. Identifying sub-populations who will benefit from ketamine, as well those may not, prior treatment initiation, would significantly advance precision medicine with MDD. Here, we mass spectrometry-based plasma proteomics analyze matched pre- post-ketamine samples a cohort 30 whose outcomes demographic clinical characteristics were considered. responders non-responders identified according their individual after two weeks We analyzed proteomic alterations post-treatment collection six proteins pivotal the antidepressive ketamine. Subsequent co-regulation analysis revealed that pathways related immune response involved response. By comparing profiles same individuals at time points, dynamic rearrangements induced immune-related processes activated association effect. Furthermore, receiver operating characteristic curve pre-treatment three strong predictive performance determining before receiving These findings provide valuable knowledge about response, which ultimately lead more personalized effective treatments for patients. The study was registered Chinese Clinical Trials Registry (ChiCTR-OOC-17012239) on May 26, 2017.

Язык: Английский

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