Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses DOI Creative Commons

Alyssa A Nitz,

Jose Humberto Giraldez Chavez,

Zachary G. Eliason

и другие.

Journal of Proteome Research, Год журнала: 2024, Номер unknown

Опубликована: Июль 9, 2024

Single-cell analysis is an active area of research in many fields biology. Measurements at single-cell resolution allow researchers to study diverse populations without losing biologically meaningful information sample averages. Many technologies have been used single cells, including mass spectrometry-based proteomics (SCP). SCP has seen a lot growth over the past couple years through improvements data acquisition and analysis, leading greater proteomic depth. Because method development main focus SCP, biological applications sprinkled only as proof-of-concept. However, methods now provide significant coverage proteome implemented laboratories. Thus, primary question address our community whether current state technology ready for widespread adoption inquiry. In this Perspective, we examine potential three thematic areas investigation: cell annotation, developmental trajectories, spatial mapping. We identify that limitation throughput. As depth target date, advocate change facilitate measuring tens thousands proteomes enable beyond

Язык: Английский

The 2023 Report on the Proteome from the HUPO Human Proteome Project DOI
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall

и другие.

Journal of Proteome Research, Год журнала: 2024, Номер 23(2), С. 532 - 549

Опубликована: Янв. 17, 2024

Since 2010, the Human Proteome Project (HPP), flagship initiative of Organization (HUPO), has pursued two goals: (1) to credibly identify protein parts list and (2) make proteomics an integral part multiomics studies human health disease. The HPP relies on international collaboration, data sharing, standardized reanalysis MS sets by PeptideAtlas MassIVE-KB using Guidelines for quality assurance, integration curation non-MS neXtProt, plus extensive use antibody profiling carried out Protein Atlas. According neXtProt release 2023-04-18, expression now been detected (PE1) 18,397 19,778 predicted proteins coded in genome (93%). Of these PE1 proteins, 17,453 were with mass spectrometry (MS) accordance 944 a variety methods. number PE2, PE3, PE4 missing stands at 1381. Achieving unambiguous identification 93% encoded from across all chromosomes represents remarkable experimental progress list. Meanwhile, there are several categories that have proved resistant detection regardless protein-based methods used. Additionally some PE1–4 probably should be reclassified PE5, specifically 21 LINC entries ∼30 HERV entries; being addressed present year. Applying wide array biological clinical ensures other omics platforms as reported Biology Disease-driven teams pathology resource pillars. Current positioned transition its Grand Challenge focused determining primary function(s) every itself networks pathways within context

Язык: Английский

Процитировано

15
MS2Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0 DOI
Louise Marie Buur, Arthur Declercq,

Marina Strobl

и другие.

Journal of Proteome Research, Год журнала: 2024, Номер 23(8), С. 3200 - 3207

Опубликована: Март 16, 2024

Rescoring of peptide-spectrum matches (PSMs) has emerged as a standard procedure for the analysis tandem mass spectrometry data. This emphasizes need software maintenance and continuous improvement such algorithms. We introduce MS

Язык: Английский

Процитировано

14
The maintenance of oocytes in the mammalian ovary involves extreme protein longevity DOI Creative Commons
Katarina Harasimov, Rebecca L. Gorry, Luisa M. Welp

и другие.

Nature Cell Biology, Год журнала: 2024, Номер 26(7), С. 1124 - 1138

Опубликована: Июнь 20, 2024

Abstract Women are born with all of their oocytes. The oocyte proteome must be maintained minimal damage throughout the woman’s reproductive life, and hence for decades. Here we report that ovarian proteostasis involves extreme protein longevity. Mouse ovaries had more extremely long-lived proteins than other tissues, including brain. These diverse functions, in mitochondria, cytoskeleton, chromatin proteostasis. stable resided not only oocytes but also somatic cells. Our data suggest mammals increase longevity enhance by chaperones cellular antioxidants to maintain female germline long periods. Indeed, aggregation did age proteasome activity decay. However, increasing cannot fully block senescence. Large-scale profiling ~8,890 revealed a decline many network aging ovary, accompanied massive remodeling, which eventually leads fertility decline.

Язык: Английский

Процитировано

12
Comparative proteomic landscapes elucidate human preimplantation development and failure DOI
Wencheng Zhu, Juan Meng, Yán Li

и другие.

Cell, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

1
A critical evaluation of ultrasensitive single-cell proteomics strategies DOI
Mary Rachel Nalehua, Joseph Zaia

Analytical and Bioanalytical Chemistry, Год журнала: 2024, Номер 416(9), С. 2359 - 2369

Опубликована: Фев. 15, 2024

Язык: Английский

Процитировано

7
Label Free Assessment of Key Biological Autofluorophores: Material Characteristics and Opportunities for Clinical Applications DOI
Jared M. Campbell,

Martin E. Gosnell,

Adnan Agha

и другие.

Advanced Materials, Год журнала: 2024, Номер unknown

Опубликована: Май 22, 2024

Autofluorophores are endogenous fluorescent compounds that naturally occur in the intra and extracellular spaces of all tissues organs. Most have vital biological functions - like metabolic cofactors NAD(P)H FAD

Язык: Английский

Процитировано

6
Graph neural networks for single-cell omics data: a review of approaches and applications DOI Creative Commons

Shiming Li,

Heyang Hua, Shengquan Chen

и другие.

Briefings in Bioinformatics, Год журнала: 2025, Номер 26(2)

Опубликована: Март 1, 2025

Abstract Rapid advancement of sequencing technologies now allows for the utilization precise signals at single-cell resolution in various omics studies. However, massive volume, ultra-high dimensionality, and high sparsity nature data have introduced substantial difficulties to traditional computational methods. The intricate non-Euclidean networks intracellular intercellular signaling molecules within datasets, coupled with complex, multimodal structures arising from multi-omics joint analysis, pose significant challenges conventional deep learning operations reliant on Euclidean geometries. Graph neural (GNNs) extended data, allowing cells their features datasets be modeled as nodes a graph structure. GNNs been successfully applied across broad range tasks analysis. In this survey, we systematically review 107 successful applications six variants tasks. We begin by outlining fundamental principles variants, followed systematic GNN-based models epigenomics, transcriptomics, spatial proteomics, multi-omics. each section dedicated specific type, summarized publicly available commonly utilized articles reviewed that section, totaling 77 datasets. Finally, summarize potential shortcomings current research explore directions future anticipate will serve guiding resource researchers deepen application omics.

Язык: Английский

Процитировано

0
Human diet‐derived polyphenolic compounds and hepatic diseases: From therapeutic mechanisms to clinical utilization DOI
Qichao Hu, Wenwen Zhang, Feng Wei

и другие.

Phytotherapy Research, Год журнала: 2023, Номер 38(1), С. 280 - 304

Опубликована: Окт. 23, 2023

Abstract This review focuses on the potential ameliorative effects of polyphenolic compounds derived from human diet hepatic diseases. It discusses molecular mechanisms and recent advancements in clinical applications. Edible polyphenols have been found to play a therapeutic role, particularly liver injury, fibrosis, NAFLD/NASH, HCC. In regulation exhibit anti‐inflammatory antioxidant effects, primarily targeting TGF‐β, NF‐κB/TLR4, PI3K/AKT, Nrf2/HO‐1 signaling pathways. effectively reverse fibrotic process by inhibiting activation stellate cells (HSC). Furthermore, show efficacy against NAFLD/NASH lipid oxidation accumulation, mediated through AMPK, SIRT, PPARγ Moreover, several anti‐HCC activity suppressing tumor cell proliferation metastasis. inhibition involves blocking Akt Wnt signaling, as well epithelial‐mesenchymal transition (EMT). Additionally, trials nutritional evidence support notion that certain can improve disease associated metabolic disorders. However, further fundamental research are warranted validate dietary polyphenols.

Язык: Английский

Процитировано

11
Proteomics—The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience DOI Creative Commons
Jens R. Coorssen, Matthew P. Padula

Proteomes, Год журнала: 2024, Номер 12(2), С. 14 - 14

Опубликована: Апрель 19, 2024

With growing recognition and acknowledgement of the genuine complexity proteomes, we are finally entering post-proteogenomic era. Routine assessment proteomes as inferred correlates gene sequences (i.e., canonical ‘proteins’) cannot provide necessary critical analysis systems-level biology that is needed to understand underlying molecular mechanisms pathways or identify most selective biomarkers therapeutic targets. These requirements demand at level proteoforms/protein species, actual active players. Currently, only highly refined integrated integrative top-down proteomics (iTDP) enables analytical depth routine, comprehensive, quantitative proteome assessments across widest range proteoforms inherent native systems. Here a broad perspective field, taking in historical current realities, establish more balanced understanding where field has come from (in particular during ten years since Proteomes was launched), issues, how things likely need proceed if deep analyses succeed. We base this our firm belief best proteomic reflect, closely possible, sample moment sampling. also seek emphasise future approaches based on exploitation complementarity currently successful approaches. This emphasises continuously evaluate further optimize established approaches, avoid complacency thinking expectations but promote careful development introduction new notably those address proteoforms. Above all, wish rigorous focus quality must override largely values speed; latter would certainly be nice, could thus effectively, routinely, quantitatively assessed. Alas, composed proteoforms, not species can amplified directly mirror genes ‘canonical’). The problem hard, accept it such, payoff playing longer game promise far biomarkers, drug targets, truly personalised even individualised medicine.

Язык: Английский

Процитировано

4
Comprehensive review on single-cell RNA sequencing: A new frontier in Alzheimer's disease research DOI
Wengang Jin, Jinjin Pei, Jeane Rebecca Roy

и другие.

Ageing Research Reviews, Год журнала: 2024, Номер 100, С. 102454 - 102454

Опубликована: Авг. 12, 2024

Язык: Английский

Процитировано

4