Comparative Proteomics and N-Glycoproteomics Reveal the Effects of Different Plasma Protein Enrichment Technologies DOI

Huohuan Tian,

Ze Tao, Wanli Zhang

et al.

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: 24(1), P. 134 - 143

Published: Dec. 13, 2024

Human plasma proteomic and glycoproteomic analyses have emerged as an alternate avenue to identify disease biomarkers therapeutic approaches. However, the vast number of high-abundance proteins in can cause mass spectrometry (MS) suppression, which makes it challenging detect low-abundance (LAP). Currently, immunoaffinity-based depletion methods strategies involving nanomaterial protein coronas been developed remove (HAP) enhance depth identification. Despite these advancements, there is a lack systematic comparison evaluation qualitative quantitative effects different on human proteome glycoproteome. In this study, we evaluated performance four including combinatorial peptide ligand libraries (CPLL), Top 2, 14, corona formed by magnetic nanoparticles (MN) both proteomics N-glycoproteomics. Compared CPLL, 14 strategies, MN approach significantly increased identified peptides proteins. demonstrated relatively lower efficacy identifying intact N-glycopeptides N-glycoproteins. contrast, are better suited glycoproteomics due higher identification numbers. We believe that work provides valuable insights options for various research objectives, well clinical applications.

Language: Английский

Quantitative N-glycoproteomic analysis reveals glycosylation signatures of plasma immunoglobulin G in systemic sclerosis DOI Creative Commons
Cheng Lu,

Yanhong Li,

Yu Zhou

et al.

Frontiers in Immunology, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 7, 2025

Systemic sclerosis (SSc) is a perplexing autoimmune disorder, characterized by mysterious causes, high mortality rates, and lack of effective treatments. The role abnormal glycosylation in the onset diseases has been recognized for some time. Nonetheless, intricate details intact glycopeptides SSc remain elusive owing to challenges their detection. In this study, we plasma immunoglobulin G (IgG) N-glycopeptides from 30 patients healthy controls (HCs) via our recently developed glycopeptide analysis method GlycoQuant. Through approach, twelve differentially expressed were identified. correlation specific with clinical features was analyzed. results revealed notable increase levels 6 (IgG2-N3H3F1, IgG2-N3H4F1, IgG2-N4H4F1, IgG2-N4H5F1, IgG2-N5H4F1, IgG2-N5H5F1) decrease another set (IgG1-N4H3F1, IgG2-N3H6F1A1, IgG2-N4H4F1A1, IgG2-N5H3F1, IgG3-N4H3F1, IgG3-N4H4F1). These changes are associated various aspects SSc, including diffuse (dSSc), interstitial lung disease (ILD), progression, cardiovascular involvement C-reactive protein peripheral blood. summary, study offers detailed overview N-glycopeptide profile blood providing valuable insights that could propel further research into SSc.

Language: Английский

Citations

1
Enhanced Analysis of Low-Abundance Proteins in Soybean Seeds Using Advanced Mass Spectrometry DOI Open Access
Bo Meng, Yuan‐Yuan Huang,

Lu Ao

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(3), P. 949 - 949

Published: Jan. 23, 2025

This study presents an advanced approach for the comprehensive analysis of low-abundance proteins in soybean seeds, addressing challenges posed by high-abundance storage proteins. We compared effectiveness Data-Dependent Acquisition (DDA), Data-Independent (DIA), and BoxCar mass spectrometry techniques to identify two types seeds: High-Oil High-Protein seeds. The results indicate that DIA method, particularly methods, significantly improve detection DDA, offering deeper insights into seed biology. Specifically, BoxCar-based revealed distinct proteomic differences between highlighting more active metabolic processes Additionally, several key were identified annotated as uniquely expressed either or These findings emphasize importance techniques, such BoxCar, deepening our understanding biology supporting breeding strategies nutritional qualities.

Language: Английский

Citations

0
Deciphering N-Glycosylation Dynamics of Serum Monoclonal Immunoglobulins in Multiple Myeloma via EThcD-sceHCD-MS/MS DOI
Huixian Li,

Wanhong Lu,

Jin Qian

et al.

Journal of Proteome Research, Journal Year: 2025, Volume and Issue: unknown

Published: April 9, 2025

Serum glycoprotein glycosylation changes can indicate disease onset and progression. However, the site-specific N-glycosylation of monoclonal immunoglobulins (M-proteins) in multiple myeloma (MM) its clinical implications are unclear. In this study, we isolated pathogenic micromonoclonal IgA or IgG (approximately 2 μg) from IgA-MM patients (n = 22) IgG-MM 30), normal polyclonal healthy controls (HCs) 16). Using EThcD-sceHCD-MS/MS, dynamics serum M-proteins MM were determined. Compared with IgA1 HCs, had higher fucosylation (58.1% vs 32.1%, p < 0.001), sialylation (68.0% 50.8%, 0.011), mannosylation (1.5% 0.3%, 0.001). While, IgG1 (97.8% 95.3%, addition, specific N-glycan abundances correlated features: for IgA1, HexNAc5Hex5Fuc1NeuAc1 was associated hypocomplementemia; IgG1, HexNAc4Hex3Fuc1 albumin level (r -0.363, 0.049) estimated glomerular filtration rate -0.433, 0.017); HexNAc4Hex5 therapeutic prognosis. conclusion, their isotypes HCs have distinct profiles, N-glycans characteristics

Language: Английский

Citations

0
GlycoIP: an integrated platform for simultaneous and site-specific N/O-glycosylation analysis of human semen DOI Creative Commons
Guoyong Yan, Fei Cai, Keqiang Wu

et al.

Frontiers in Chemistry, Journal Year: 2025, Volume and Issue: 13

Published: May 19, 2025

Protein glycosylation plays a pivotal role in human semen, influencing various processes, such as spermatogenesis, maturation, sperm motility, capacitation, and fertilization. Despite its importance, the specific details regarding N/O- within semen proteins have largely remained unknown. To address this challenge, an integrated glycoproteomic platform (termed GlycoIP) was developed, enabling simultaneous analysis of both intact N- O- glycopeptides directly from samples. Characterizing these is particularly challenging, yet it provides invaluable insights into structure function glycans their attachment sites. In study, our enabled identification 1,833 unique 720 glycopeptides. This approach revealed extensive precise site-specific data, highlighting 438 potential sites 148 distinct glycoproteins. Notably, we conducted profiling on several glycoproteins, including equatorial segment protein 1 (SPESP1), which located sperm, plasma serine protease inhibitor (SERPINA5), presented seminal plasma. summary, promising for comprehensive single experiment. advancement paves way further functional studies glycoproteins roles male infertility, enhancing understanding complex field.

Language: Английский

Citations

0
GlycoPCT: Pressure Cycling Technology-Based Quantitative Glycoproteomics Reveals Distinctive N-Glycosylation in Human Liver Biopsy Samples of Nonalcoholic Fatty Liver Disease DOI
Wei Jiang, Min Liu, Tao Su

et al.

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: 24(1), P. 202 - 209

Published: Nov. 27, 2024

Protein N-glycosylation is vital in the human liver and influences functions such as lipid metabolism, apoptosis, inflammation. However, site-specific patterns variations biopsy samples between healthy individuals those with nonalcoholic fatty disease (NAFLD) remain incompletely characterized, primarily due to limitations of current clinical glycoproteomic methods, including a large demand for samples, low efficiency tissue protein extraction, recovery rate intact N-glycopeptides (IGPs). To address this issue, we developed GlycoPCT, quantitative method based on pressure cycling technology. It enables efficient IGPs accurate analysis trace samples. Our research revealed total 4,459 unique 361 glycans from 758 glycoproteins. High-mannose type, complex fucosylation sialylation type N-glycans were significantly upregulated NAFLD group (p < 0.001, t test). Notably, also identified 182 67 proteins 0.05, FC > 1.50) 108 downregulated 44 0.67) group. Furthermore, highlighted an essential acute phase glycoprotein, alpha-1-acid glycoprotein 1 (A1TA), which synthesized plays significant role progression. These novel glyco-signatures provide crucial clues diagnosis pathogenesis NAFLD.

Language: Английский

Citations

1
Quantitative site-specific N-glycosylation analysis reveals IgG glyco-signatures for pancreatic cancer diagnosis DOI Creative Commons
Yizheng Jin, Ran Hu, Yufan Gu

et al.

Clinical Proteomics, Journal Year: 2024, Volume and Issue: 21(1)

Published: Dec. 1, 2024

Pancreatic cancer is a highly aggressive tumor with poor prognosis due to low early detection rate and lack of biomarkers. Most pancreatic ductal adenocarcinoma (PDAC). Alterations in the N-glycosylation plasma immunoglobulin G (IgG) have been shown be closely associated onset development several cancers could used as biomarkers for diagnosis. The study aimed explore intact profile IgG patients PDAC find relation between clinical information such diagnosis prognosis.

Language: Английский

Citations

1
Site-Specific Quantitative N-Glycoproteomics: The Great Clinical Application Potential of GlycoQuant DOI
Hao Yang, Ganglong Yang, Jicheng Lv

et al.

Phenomics, Journal Year: 2024, Volume and Issue: 4(4), P. 394 - 396

Published: July 29, 2024

Language: Английский

Citations

0
ProteoNet: A CNN-based Framework for Analyzing Proteomics MS-RGB Images DOI Creative Commons
Jinze Huang, Yimin Li, Bo Meng

et al.

iScience, Journal Year: 2024, Volume and Issue: 27(12), P. 111362 - 111362

Published: Nov. 12, 2024

Proteomics is crucial in clinical research, yet the application of proteomic data remains challenging. Transforming mass spectrometry (MS) into red, green, and blue color (MS-RGB) image formats applying deep learning (DL) techniques has shown great potential to enhance analysis efficiency. However, current DL models often fail extract subtle, features from MS-RGB data. To address this, we developed ProteoNet, a framework that refines analysis. ProteoNet incorporates semantic partitioning, adaptive average pooling, weighted factors Convolutional Neural Network (CNN) model, thus enhancing accuracy. Our experiments with proteomics urine, blood, tissue samples related liver, kidney, thyroid diseases demonstrate outperforms existing also provides direct conversion method for data, enabling seamless workflow. Moreover, its compatibility various CNN architectures, including lightweight like MobileNetV2, underscores scalability potential.

Language: Английский

Citations

0
Tools and techniques for quantitative glycoproteomic analysis DOI
Siyuan Kong, Wei Zhang, Weiqian Cao

et al.

Biochemical Society Transactions, Journal Year: 2024, Volume and Issue: 52(6), P. 2439 - 2453

Published: Dec. 10, 2024

Recent advances in mass spectrometry (MS)-based methods have significantly expanded the capabilities for quantitative glycoproteomics, enabling highly sensitive and accurate quantitation of glycosylation at intact glycopeptide level. These developments provided valuable insights into roles glycoproteins various biological processes diseases. In this short review, we summarize pertinent studies on techniques tools site-specific glycoproteomic analysis published over past decade. We also highlight state-of-the-art MS-based software that facilitate multi-dimension quantification glycoproteome, targeted specific glycopeptides, isomers. Additionally, discuss potential applications these technologies clinical biomarker discovery functional characterization health disease. The review concludes with a discussion current challenges future perspectives field, emphasizing need more precise, high-throughput efficient to further advance glycoproteomics its applications.

Language: Английский

Citations

0
Comparative Proteomics and N-Glycoproteomics Reveal the Effects of Different Plasma Protein Enrichment Technologies DOI

Huohuan Tian,

Ze Tao, Wanli Zhang

et al.

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: 24(1), P. 134 - 143

Published: Dec. 13, 2024

Human plasma proteomic and glycoproteomic analyses have emerged as an alternate avenue to identify disease biomarkers therapeutic approaches. However, the vast number of high-abundance proteins in can cause mass spectrometry (MS) suppression, which makes it challenging detect low-abundance (LAP). Currently, immunoaffinity-based depletion methods strategies involving nanomaterial protein coronas been developed remove (HAP) enhance depth identification. Despite these advancements, there is a lack systematic comparison evaluation qualitative quantitative effects different on human proteome glycoproteome. In this study, we evaluated performance four including combinatorial peptide ligand libraries (CPLL), Top 2, 14, corona formed by magnetic nanoparticles (MN) both proteomics N-glycoproteomics. Compared CPLL, 14 strategies, MN approach significantly increased identified peptides proteins. demonstrated relatively lower efficacy identifying intact N-glycopeptides N-glycoproteins. contrast, are better suited glycoproteomics due higher identification numbers. We believe that work provides valuable insights options for various research objectives, well clinical applications.

Language: Английский

Citations

0