LIVIVO - Search results -

Search results

Result 1 - 10 of total 131

Search options

Article: Correction: A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples.

Mangalaparthi, Kiran K / Chavan, Sandip / Madugundu, Anil K / Renuse, Santosh / Vanderboom, Patrick M / Maus, Anthony D / Kemp, Jennifer / Kipp, Benjamin R / Grebe, Stefan K / Singh, Ravinder J / Pandey, Akhilesh

Clinical proteomics

2022 Volume 19, Issue 1, Page(s) 11

Language	English
Publishing date	2022-05-04
Publishing country	England
Document type	Published Erratum
ZDB-ID	2205154-5
ISSN	1542-6416
ISSN	1542-6416
DOI	10.1186/s12014-022-09355-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6222: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition.

Nature biotechnology

2024

Abstract: Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here we present the narrow-window data-independent acquisition (nDIA) strategy consisting of high-resolution MS1 scans with parallel ... ...

Abstract	Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here we present the narrow-window data-independent acquisition (nDIA) strategy consisting of high-resolution MS1 scans with parallel tandem MS (MS/MS) scans of ~200 Hz using 2-Th isolation windows, dissolving the differences between data-dependent and -independent methods. This is achieved by pairing a quadrupole Orbitrap mass spectrometer with the asymmetric track lossless (Astral) analyzer which provides >200-Hz MS/MS scanning speed, high resolving power and sensitivity, and low-ppm mass accuracy. The nDIA strategy enables profiling of >100 full yeast proteomes per day, or 48 human proteomes per day at the depth of ~10,000 human protein groups in half-an-hour or ~7,000 proteins in 5 min, representing 3× higher coverage compared with current state-of-the-art MS. Multi-shot acquisition of offline fractionated samples provides comprehensive coverage of human proteomes in ~3 h. High quantitative precision and accuracy are demonstrated in a three-species proteome mixture, quantifying 14,000+ protein groups in a single half-an-hour run.
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-023-02099-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 137: Show issues
Zs.MG 43: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Cerebrospinal fluid lipidomics for biomarkers of Alzheimer's disease.

Byeon, Seul Kee / Madugundu, Anil K / Jain, Ankit P / Bhat, Firdous A / Jung, Jae Hun / Renuse, Santosh / Darrow, Jacqueline / Bakker, Arnold / Albert, Marilyn / Moghekar, Abhay / Pandey, Akhilesh

Molecular omics

2022 Volume 17, Issue 3, Page(s) 454–463

Abstract: Alzheimer's disease (AD) is the most common cause of dementia and is associated with serious neurologic sequelae resulting from neurodegenerative changes. Identification of markers of early-stage AD could be important for designing strategies to arrest ... ...

Abstract	Alzheimer's disease (AD) is the most common cause of dementia and is associated with serious neurologic sequelae resulting from neurodegenerative changes. Identification of markers of early-stage AD could be important for designing strategies to arrest the progression of the disease. The brain is rich in lipids because they are crucial for signal transduction and anchoring of membrane proteins. Cerebrospinal fluid (CSF) is an excellent specimen for studying the metabolism of lipids in AD because it can reflect changes occurring in the brain. We aimed to identify CSF lipidomic alterations associated with AD, using untargeted lipidomics, carried out in positive and negative ion modes. We found CSF lipids that were significantly altered in AD cases. In addition, comparison of CSF lipid profiles between persons with mild cognitive impairment (MCI) and AD showed a strong positive correlation between the lipidomes of the MCI and AD groups. The novel lipid biomarkers identified in this study are excellent candidates for validation in a larger set of patient samples and as predictive biomarkers of AD through future longitudinal studies. Once validated, the lipid biomarkers could lead to early detection, disease monitoring and the ability to measure the efficacy of potential therapeutic interventions in AD.
MeSH term(s)	Aged ; Aged, 80 and over ; Alzheimer Disease/cerebrospinal fluid ; Alzheimer Disease/metabolism ; Biomarkers/cerebrospinal fluid ; Case-Control Studies ; Chromatography, High Pressure Liquid ; Cognitive Dysfunction/cerebrospinal fluid ; Cognitive Dysfunction/metabolism ; Female ; Humans ; Lipidomics/methods ; Lipids/cerebrospinal fluid ; Male ; Middle Aged ; Tandem Mass Spectrometry
Chemical Substances	Biomarkers ; Lipids
Language	English
Publishing date	2022-10-26
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2515-4184
ISSN (online)	2515-4184
DOI	10.1039/d0mo00186d
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: 13

Renuse, Santosh / Benson, Linda M / Vanderboom, Patrick M / Ruchi, F N U / Yadav, Yogesh R / Johnson, Kenneth L / Brown, Benjamin C / Peterson, Jane A / Basu, Rita / McCormick, Daniel J / Pandey, Akhilesh / Basu, Ananda

Clinical proteomics

2022 Volume 19, Issue 1, Page(s) 16

Abstract: Background: Glucagon serves as an important regulatory hormone for regulating blood glucose concentration with tight feedback control exerted by insulin and glucose. There are critical gaps in our understanding of glucagon kinetics, pancreatic α cell ... ...

Abstract	Background: Glucagon serves as an important regulatory hormone for regulating blood glucose concentration with tight feedback control exerted by insulin and glucose. There are critical gaps in our understanding of glucagon kinetics, pancreatic α cell function and intra-islet feedback network that are disrupted in type 1 diabetes. This is important for translational research applications of evolving dual-hormone (insulin + glucagon) closed-loop artificial pancreas algorithms and their usage in type 1 diabetes. Thus, it is important to accurately measure glucagon kinetics in vivo and to develop robust models of glucose-insulin-glucagon interplay that could inform next generation of artificial pancreas algorithms. Methods: Here, we describe the administration of novel Results: The limit of quantitation was found to be 1.56 pg/ml using stable isotope-labeled glucagon as an internal standard. Intra and inter-assay variability was < 6% and < 16%, respectively, for FF glucagon while it was < 5% and < 23%, respectively, for FFLA glucagon. Further, we carried out a novel isotope dilution technique using glucagon tracers for studying glucagon kinetics in type 1 diabetes. Conclusions: The methods described in this study for simultaneous detection and quantitation of glucagon tracers have clinical utility for investigating glucagon kinetics in vivo in humans.
Language	English
Publishing date	2022-05-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2205154-5
ISSN	1542-6416
ISSN	1542-6416
DOI	10.1186/s12014-022-09344-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6222: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Machine Learning-Based Fragment Selection Improves the Performance of Qualitative PRM Assays.

Vanderboom, Patrick M / Renuse, Santosh / Maus, Anthony D / Madugundu, Anil K / Kemp, Jennifer V / Gurtner, Kari M / Singh, Ravinder J / Grebe, Stefan K / Pandey, Akhilesh / Dasari, Surendra

Journal of proteome research

2022 Volume 21, Issue 8, Page(s) 2045–2054

Abstract: Targeted mass spectrometry-based platforms have become a valuable tool for the sensitive and specific detection of protein biomarkers in clinical and research settings. Traditionally, developing a targeted assay for peptide quantification has involved ... ...

Abstract	Targeted mass spectrometry-based platforms have become a valuable tool for the sensitive and specific detection of protein biomarkers in clinical and research settings. Traditionally, developing a targeted assay for peptide quantification has involved manually preselecting several fragment ions and establishing a limit of detection (LOD) and a lower limit of quantitation (LLOQ) for confident detection of the target. Established thresholds such as LOD and LLOQ, however, inherently sacrifice sensitivity to afford specificity. Here, we demonstrate that machine learning can be applied to qualitative PRM assays to discriminate positive from negative samples more effectively than a traditional approach utilizing conventional methods. To demonstrate the utility of this method, we trained an ensemble machine learning model using 282 SARS-CoV-2 positive and 994 SARS-CoV-2 negative nasopharyngeal swabs (NP swab) analyzed using a targeted PRM method. This model was then validated using an independent set of 200 positive and 150 negative samples and achieved a sensitivity of 92% relative to results obtained by RT-PCR, which was superior to a traditional approach that resulted in 86.5% sensitivity when analyzing the same data. These results demonstrate that machine learning can be applied to qualitative PRM assays and results in superior performance relative to traditional methods.
MeSH term(s)	COVID-19 ; COVID-19 Testing ; Humans ; Machine Learning ; Mass Spectrometry/methods ; SARS-CoV-2 ; Sensitivity and Specificity
Language	English
Publishing date	2022-07-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00156
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6189: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Generation and proteome profiling of PBMC-originated, iPSC-derived lentoid bodies.

Ali, Muhammad / Kabir, Firoz / Raskar, Snehal / Renuse, Santosh / Na, Chan Hyun / Delannoy, Michael / Khan, Shahid Y / Riazuddin, S Amer

Stem cell research

2020 Volume 46, Page(s) 101813

Abstract: Here, we report proteome profiling of peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cell (iPSC)-derived, lens-like organoids termed lentoid bodies at two differentiation time points. A small aliquot of the blood sample was ...

Abstract	Here, we report proteome profiling of peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cell (iPSC)-derived, lens-like organoids termed lentoid bodies at two differentiation time points. A small aliquot of the blood sample was ascertained to collect PBMCs that were reprogrammed to iPSCs. The PBMC-originated, iPSCs were differentiated to lentoid bodies employing the "fried egg" method. Quantitative real-time PCR (qRT-PCR) analysis revealed increased expression levels of lens-associated markers in lentoid bodies while transmission electron microscopy identified closely packed lens epithelial- and differentiating fiber-like cells in lentoid bodies. Total cellular protein was extracted from lentoid bodies at differentiation day 25 and mass spectrometry identified a total of 9,473 proteins. The low counts of crystallin proteins at differentiation day 25 prompted us to re-examine the proteome at differentiation day 35 as we reasoned that 10 additional days of differentiation will increase the crystallin count. However, we did not detect any substantial increase in crystallin protein counts at differentiation day 35. In conclusion, we report generation and proteome profiles of PBMC-originated, iPSC-derived lentoid bodies at multiple differentiation time points.
MeSH term(s)	Cell Differentiation ; Crystallins ; Induced Pluripotent Stem Cells ; Lens, Crystalline ; Leukocytes, Mononuclear ; Proteome
Chemical Substances	Crystallins ; Proteome
Language	English
Publishing date	2020-05-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1876-7753
ISSN (online)	1876-7753
DOI	10.1016/j.scr.2020.101813
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: Integrative phosphoproteome and interactome analysis of the role of Ubash3b in BCR-ABL signaling.

Cutler, Jevon A / Udainiya, Savita / Madugundu, Anil K / Renuse, Santosh / Xu, Yaoyu / Jung, Jaehun / Kim, Kwang Pyo / Wu, Xinyan / Pandey, Akhilesh

Leukemia

2019 Volume 34, Issue 1, Page(s) 301–305

MeSH term(s)	Fusion Proteins, bcr-abl/metabolism ; Humans ; Leukemia/metabolism ; Protein Tyrosine Phosphatases/metabolism ; Proteomics/methods ; Signal Transduction/physiology
Chemical Substances	Fusion Proteins, bcr-abl (EC 2.7.10.2) ; Protein Tyrosine Phosphatases (EC 3.1.3.48) ; UBASH3B protein, human (EC 3.1.3.48)
Language	English
Publishing date	2019-08-09
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	807030-1
ISSN	1476-5551 ; 0887-6924
ISSN (online)	1476-5551
ISSN	0887-6924
DOI	10.1038/s41375-019-0535-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2295: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Endoxifen downregulates AKT phosphorylation through protein kinase C beta 1 inhibition in ERα+ breast cancer.

NPJ breast cancer

2023 Volume 9, Issue 1, Page(s) 101

Abstract: Endoxifen, a secondary tamoxifen metabolite, is a potent antiestrogen exhibiting estrogen receptor alpha (ERα) binding at nanomolar concentrations. Phase I/II clinical trials identified clinical activity of Z-endoxifen (ENDX), in endocrine-refractory ... ...

Abstract	Endoxifen, a secondary tamoxifen metabolite, is a potent antiestrogen exhibiting estrogen receptor alpha (ERα) binding at nanomolar concentrations. Phase I/II clinical trials identified clinical activity of Z-endoxifen (ENDX), in endocrine-refractory metastatic breast cancer as well as ERα+ solid tumors, raising the possibility that ENDX may have a second, ERα-independent, mechanism of action. An unbiased mass spectrometry approach revealed that ENDX concentrations achieved clinically with direct ENDX administration (5 µM), but not low concentrations observed during tamoxifen treatment (<0.1 µM), profoundly altered the phosphoproteome of the aromatase expressing MCF7AC1 cells with limited impact on the total proteome. Computational analysis revealed protein kinase C beta (PKCβ) and protein kinase B alpha or AKT1 as potential kinases responsible for mediating ENDX effects on protein phosphorylation. ENDX more potently inhibited PKCβ1 kinase activity compared to other PKC isoforms, and ENDX binding to PKCβ1 was confirmed using Surface Plasma Resonance. Under conditions that activated PKC/AKT signaling, ENDX induced PKCβ1 degradation, attenuated PKCβ1-activated AKT
Language	English
Publishing date	2023-12-19
Publishing country	United States
Document type	Journal Article
ISSN	2374-4677
ISSN	2374-4677
DOI	10.1038/s41523-023-00606-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Comparison of anti-peptide and anti-protein antibody-based purification techniques for detection of SARS-CoV-2 by targeted LC-MS/MS

Anthony Maus / Santosh Renuse / Jennifer Kemp / Kayla Moehnke / Kiran K. Mangalaparthi / Sandip Chavan / Anil K. Madugundu / Patrick M. Vanderboom / Surendra Dasari / Benjamin R. Kipp / Ravinder J. Singh / Stefan K. Grebe / Akhilesh Pandey

Advances in Sample Preparation, Vol 2, Iss , Pp 100018- (2022)

2022

Abstract: ABSTRACT: The COVID-19 pandemic has necessitated exploration of alternative testing methods for detection of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) to ensure clinical laboratories can continue to provide critical testing results. ... ...

Abstract	ABSTRACT: The COVID-19 pandemic has necessitated exploration of alternative testing methods for detection of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) to ensure clinical laboratories can continue to provide critical testing results. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is established in many clinical laboratories due its high specificity and sensitivity, making it a logical alternative methodology. However, matching the sensitivity of quantitative reverse transcription-polymerase chain reaction (qRT-PCR) remains challenging, which forced utilization of antibody-based enrichment prior to targeted LC-MS/MS analysis. When utilizing antibody purification techniques, investigators must decide whether to enrich the target protein or peptides, but there are few studies comparing the two approaches to assist in this decision-making process. In this work, we present a comparison of intact protein and peptide antibody-based purification for LC-MS/MS based detection of SARS-CoV-2. We have found that protein purification yields more intense LC-MS/MS signals, but is also less specific, yielding higher noise and more background when compared to peptide purification techniques. Therefore, when using traditional data analysis techniques, the enrichment technique that provides superior sensitivity varies for individual peptides and no definitive overall conclusion can be made. These observations are corroborated when using a novel machine learning approach to determine positive/negative test results, which yielded superior sensitivity when using protein purification, but better specificity and area under the ROC curve when performing peptide purification.
Keywords	Nucleocapsid protein ; SARS-CoV-2 ; Antibody-based enrichment ; Immunopurification ; Tandem mass spectrometry ; Chemistry ; QD1-999
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Quantitative Tyrosine Phosphoproteome Profiling of AXL Receptor Tyrosine Kinase Signaling Network.

Wu, Xinyan / Wang, Li / Pearson, Nicole A / Renuse, Santosh / Cheng, Ran / Liang, Ye / Mun, Dong-Gi / Madugundu, Anil K / Xu, Yaoyu / Gill, Parkash S / Pandey, Akhilesh

Cancers

2021 Volume 13, Issue 16

Abstract: Overexpression and amplification of AXL receptor tyrosine kinase (RTK) has been found in several hematologic and solid malignancies. Activation of AXL can enhance tumor-promoting processes such as cancer cell proliferation, migration, invasion and ... ...

Abstract	Overexpression and amplification of AXL receptor tyrosine kinase (RTK) has been found in several hematologic and solid malignancies. Activation of AXL can enhance tumor-promoting processes such as cancer cell proliferation, migration, invasion and survival. Despite the important role of AXL in cancer development, a deep and quantitative mapping of its temporal dynamic signaling transduction has not yet been reported. Here, we used a TMT labeling-based quantitative proteomics approach to characterize the temporal dynamics of the phosphotyrosine proteome induced by AXL activation. We identified >1100 phosphotyrosine sites and observed a widespread upregulation of tyrosine phosphorylation induced by GAS6 stimulation. We also detected several tyrosine sites whose phosphorylation levels were reduced upon AXL activation. Gene set enrichment-based pathway analysis indicated the activation of several cancer-promoting and cell migration/invasion-related signaling pathways, including RAS, EGFR, focal adhesion, VEGFR and cytoskeletal rearrangement pathways. We also observed a rapid induction of phosphorylation of protein tyrosine phosphatases, including PTPN11 and PTPRA, upon GAS6 stimulation. The novel molecules downstream of AXL identified in this study along with the detailed global quantitative map elucidating the temporal dynamics of AXL activation should not only help understand the oncogenic role of AXL, but also aid in developing therapeutic options to effectively target AXL.
Language	English
Publishing date	2021-08-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers13164234
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito