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  1. Article ; Online: Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics.

    Bortel, Patricia / Piga, Ilaria / Koenig, Claire / Gerner, Christopher / Martinez-Val, Ana / Olsen, Jesper V

    Molecular & cellular proteomics : MCP

    2024  Volume 23, Issue 5, Page(s) 100754

    Abstract: Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental ... ...

    Abstract Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-bead phosphoproteomics sample preparation with a focus on low-input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores, and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample, and loading buffer volumes allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 μg of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA).
    Language English
    Publishing date 2024-03-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2075924-1
    ISSN 1535-9484 ; 1535-9476
    ISSN (online) 1535-9484
    ISSN 1535-9476
    DOI 10.1016/j.mcpro.2024.100754
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5599: Show issues Location:
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  2. Article: Inward Outward Signaling in Ovarian Cancer: Morpho-Phospho-Proteomic Profiling Upon Application of Hypoxia and Shear Stress Characterizes the Adaptive Plasticity of OVCAR-3 and SKOV-3 Cells.

    Bileck, Andrea / Bortel, Patricia / Kriz, Michelle / Janker, Lukas / Kiss, Endre / Gerner, Christopher / Del Favero, Giorgia

    Frontiers in oncology

    2022  Volume 11, Page(s) 746411

    Abstract: With the onset of resistance, ovarian cancer cells display almost unpredictable adaptive potential. This may derive from the tumor genetic ancestry and can be additionally tailored by post translational protein modifications (PTMs). In this study, we ... ...

    Abstract With the onset of resistance, ovarian cancer cells display almost unpredictable adaptive potential. This may derive from the tumor genetic ancestry and can be additionally tailored by post translational protein modifications (PTMs). In this study, we took advantage of high-end (phospho)-proteome analysis combined with multiparametric morphometric profiling in high-grade serous (OVCAR-3) and non-serous (SKOV-3) ovarian carcinoma cells. For functional experiments, we applied two different protocols, representing typical conditions of the abdominal cavity and of the growing tumor tissue: on the one side hypoxia (oxygen 1%) which develops within the tumor mass or is experienced during migration/extravasation in non-vascularized areas. On the other hand, fluid shear stress (250 rpm, 2.8 dyn/cm
    Language English
    Publishing date 2022-02-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2021.746411
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Gendered burial practices of early Bronze Age children align with peptide-based sex identification: A case study from Franzhausen I, Austria

    Rebay-Salisbury, Katharina / Bortel, Patricia / Janker, Lukas / Bas, Marlon / Pany-Kucera, Doris / Salisbury, Roderick B. / Gerner, Christopher / Kanz, Fabian

    Journal of archaeological science. 2022 Mar., v. 139

    2022  

    Abstract: Gendered burial practices that differentiate between men and women by the way the body was placed were used over large parts of Central Europe in the Late Neolithic and Early Bronze Age (c. 2900–1600 BC). Until recently, it was unknown if the sex-based ... ...

    Abstract Gendered burial practices that differentiate between men and women by the way the body was placed were used over large parts of Central Europe in the Late Neolithic and Early Bronze Age (c. 2900–1600 BC). Until recently, it was unknown if the sex-based differentiation of bodies was extended to children, and if the biological sex of the children matched the classification as men and women placed on the left/right side in the opposite orientation. We applied nanoflow liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) to identify sex-specific peptides in human tooth enamel in 75 children under 12 years at death buried at one of the largest Early Bronze Age cemeteries in Europe, Franzhausen I, Austria, 70 of which produced reliable results. The study confirmed that the sex of the children corresponds to the gendered body position in 98.4% of cases. For burials in which the gendered sidedness and orientation are not internally consistent with the male or female pattern, we found that the sidedness of the body corresponds to the sex of the children rather than the orientation.
    Keywords archaeology ; case studies ; death ; females ; humans ; liquid chromatography ; males ; peptides ; tandem mass spectrometry ; tooth enamel ; Austria ; Central European region
    Language English
    Dates of publication 2022-03
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1468969-8
    ISSN 0305-4403
    ISSN 0305-4403
    DOI 10.1016/j.jas.2022.105549
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Amelogenin peptide analyses reveal female leadership in Copper Age Iberia (c. 2900-2650 BC).

    Cintas-Peña, Marta / Luciañez-Triviño, Miriam / Montero Artús, Raquel / Bileck, Andrea / Bortel, Patricia / Kanz, Fabian / Rebay-Salisbury, Katharina / García Sanjuán, Leonardo

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 9594

    Abstract: Given the absence of written records, the main source of information available to analyze gender inequalities in early complex societies is the human body itself. And yet, for decades, archaeologists have struggled with the sex estimation of poorly ... ...

    Abstract Given the absence of written records, the main source of information available to analyze gender inequalities in early complex societies is the human body itself. And yet, for decades, archaeologists have struggled with the sex estimation of poorly preserved human remains. Here we present an exceptional case study that shows how ground-breaking new scientific methods may address this problem. Through the analysis of sexually dimorphic amelogenin peptides in tooth enamel, we establish that the most socially prominent person of the Iberian Copper Age (c. 3200-2200 BC) was not male, as previously thought, but female. The analysis of this woman, discovered in 2008 at Valencina, Spain, reveals that she was a leading social figure at a time where no male attained a remotely comparable social position. Only other women buried a short time after in the Montelirio tholos, part of the same burial area, appear to have enjoyed a similarly high social position. Our results invite to reconsider established interpretations about the political role of women at the onset of early social complexity, and question traditionally held views of the past. Furthermore, this study anticipates the changes that newly developed scientific methods may bring to prehistoric archaeology and the study of human social evolution.
    MeSH term(s) Humans ; Female ; Amelogenin ; Leadership ; Peptides ; Spain ; Archaeology
    Chemical Substances Amelogenin ; Peptides
    Language English
    Publishing date 2023-07-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-36368-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Multiomics-empowered Deep Phenotyping of Ulcerative Colitis Identifies Biomarker Signatures Reporting Functional Remission States.

    Janker, Lukas / Schuster, Dina / Bortel, Patricia / Hagn, Gerhard / Meier-Menches, Samuel M / Mohr, Thomas / Mader, Johanna C / Slany, Astrid / Bileck, Andrea / Brunmair, Julia / Madl, Christian / Unger, Lukas / Hennlich, Barbara / Weitmayr, Barbara / Del Favero, Giorgia / Pils, Dietmar / Pukrop, Tobias / Pfisterer, Nikolaus / Feichtenschlager, Thomas /
    Gerner, Christopher

    Journal of Crohn's & colitis

    2023  Volume 17, Issue 9, Page(s) 1514–1527

    Abstract: Introduction: Ulcerative colitis [UC] is a chronic disease with rising incidence and unclear aetiology. Deep molecular phenotyping by multiomics analyses may provide novel insights into disease processes and characteristic features of remission states.!# ...

    Abstract Introduction: Ulcerative colitis [UC] is a chronic disease with rising incidence and unclear aetiology. Deep molecular phenotyping by multiomics analyses may provide novel insights into disease processes and characteristic features of remission states.
    Methods: UC pathomechanisms were assessed by proteome profiling of human tissue specimens, obtained from five distinct colon locations for each of the 12 patients included in the study. Systemic disease-associated alterations were evaluated thanks to a cross-sectional setting of mass spectrometry-based multiomics analyses comprising proteins, metabolites, and eicosanoids of plasma obtained from UC patients during acute episodes and upon remission, in comparison with healthy controls.
    Results: Tissue proteome profiling indicated colitis-associated activation of neutrophils, macrophages, B and T cells, fibroblasts, endothelial cells and platelets, and hypoxic stress, and suggested a general downregulation of mitochondrial proteins accompanying the establishment of apparent wound healing-promoting activities including scar formation. Whereas pro-inflammatory proteins were apparently upregulated by immune cells, the colitis-associated epithelial cells, fibroblasts, endothelial cells, and platelets seemed to predominantly contribute anti-inflammatory and wound healing-promoting proteins. Blood plasma proteomics indicated chronic inflammation and platelet activation, whereas plasma metabolomics identified disease-associated deregulations of gut and gut microbiome-derived metabolites. Upon remission several, but not all, molecular candidate biomarker levels recovered back to normal.
    Conclusion: The findings may indicate that microvascular damage and platelet deregulation hardly resolve upon remission, but apparently persist as disease-associated molecular signatures. This study presents local and systemic molecular alterations integrated in a model for UC pathomechanisms, potentially supporting the assessment of disease and remission states in UC patients.
    Language English
    Publishing date 2023-03-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 2390120-2
    ISSN 1876-4479 ; 1873-9946
    ISSN (online) 1876-4479
    ISSN 1873-9946
    DOI 10.1093/ecco-jcc/jjad052
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6634: Show issues Location:
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  6. Article ; Online: Proteomic Profiling of Advanced Melanoma Patients to Predict Therapeutic Response to Anti-PD-1 Therapy.

    Zila, Nina / Eichhoff, Ossia M / Steiner, Irene / Mohr, Thomas / Bileck, Andrea / Cheng, Phil F / Leitner, Alexander / Gillet, Ludovic / Sajic, Tatjana / Goetze, Sandra / Friedrich, Betty / Bortel, Patricia / Strobl, Johanna / Reitermaier, René / Hogan, Sabrina A / Martínez Gómez, Julia M / Staeger, Ramon / Tuchmann, Felix / Peters, Sophie /
    Stary, Georg / Kuttke, Mario / Elbe-Bürger, Adelheid / Hoeller, Christoph / Kunstfeld, Rainer / Weninger, Wolfgang / Wollscheid, Bernd / Dummer, Reinhard / French, Lars E / Gerner, Christopher / Aebersold, Ruedi / Levesque, Mitchell P / Paulitschke, Verena

    Clinical cancer research : an official journal of the American Association for Cancer Research

    2023  Volume 30, Issue 1, Page(s) 159–175

    Abstract: Purpose: Despite high clinical need, there are no biomarkers that accurately predict the response of patients with metastatic melanoma to anti-PD-1 therapy.: Experimental design: In this multicenter study, we applied protein depletion and enrichment ... ...

    Abstract Purpose: Despite high clinical need, there are no biomarkers that accurately predict the response of patients with metastatic melanoma to anti-PD-1 therapy.
    Experimental design: In this multicenter study, we applied protein depletion and enrichment methods prior to various proteomic techniques to analyze a serum discovery cohort (n = 56) and three independent serum validation cohorts (n = 80, n = 12, n = 17). Further validation analyses by literature and survival analysis followed.
    Results: We identified several significantly regulated proteins as well as biological processes such as neutrophil degranulation, cell-substrate adhesion, and extracellular matrix organization. Analysis of the three independent serum validation cohorts confirmed the significant differences between responders (R) and nonresponders (NR) observed in the initial discovery cohort. In addition, literature-based validation highlighted 30 markers overlapping with previously published signatures. Survival analysis using the TCGA database showed that overexpression of 17 of the markers we identified correlated with lower overall survival in patients with melanoma.
    Conclusions: Ultimately, this multilayered serum analysis led to a potential marker signature with 10 key markers significantly altered in at least two independent serum cohorts: CRP, LYVE1, SAA2, C1RL, CFHR3, LBP, LDHB, S100A8, S100A9, and SAA1, which will serve as the basis for further investigation. In addition to patient serum, we analyzed primary melanoma tumor cells from NR and found a potential marker signature with four key markers: LAMC1, PXDN, SERPINE1, and VCAN.
    MeSH term(s) Humans ; Melanoma/drug therapy ; Melanoma/genetics ; Melanoma/metabolism ; Proteomics ; Biomarkers, Tumor/metabolism ; Survival Analysis
    Chemical Substances Biomarkers, Tumor
    Language English
    Publishing date 2023-10-20
    Publishing country United States
    Document type Multicenter Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1225457-5
    ISSN 1557-3265 ; 1078-0432
    ISSN (online) 1557-3265
    ISSN 1078-0432
    DOI 10.1158/1078-0432.CCR-23-0562
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4223: Show issues Location:
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