Blar i Faculty of Medicine på emneord "Proteomics"
Viser treff 1-16 av 16
-
Anatomy and evolution of database search engines — a central component of mass spectrometry based proteomic workflows
(Peer reviewed; Journal article, 2017-09-13)Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass ... -
Characterization of glomerular extracellular matrix in IgA nephropathy by proteomic analysis of laser-captured microdissected glomeruli
(Peer reviewed; Journal article, 2019-11-14)Background IgA nephropathy (IgAN) involves mesangial matrix expansion, but the proteomic composition of this matrix is unknown. The present study aimed to characterize changes in extracellular matrix in IgAN. Methods In ... -
Colorectal cancer derived organotypic spheroids maintain essential tissue characteristics but adapt their metabolism in culture
(Peer reviewed; Journal article, 2014-07-11)Background: Organotypic tumor spheroids, a 3D in vitro model derived from patient tumor material, preserve tissue heterogeneity and retain structural tissue elements, thus replicating the in vivo tumor more closely than ... -
Crowdsourcing in proteomics: public resources lead to better experiments
(Peer reviewed; Journal article, 2013-04)With the growing interest in the field of proteomics, the amount of publicly available proteome resources has also increased dramatically. This means that there are many useful resources available for almost all aspects ... -
Discrimination of grade 2 and 3 cervical intraepithelial neoplasia by means of analysis of water soluble proteins recovered from cervical biopsies
(Peer reviewed; Journal article, 2011-06-28)Background: Cervical intraepithelial neoplasia (CIN) grades 2 and 3 are usually grouped and treated in the same way as “high grade”, in spite of their different risk to cancer progression and spontaneous regression rates. ... -
The effect of WnT pathway modulators on human iPSC-derived pancreatic beta cell maturation
(Peer reviewed; Journal article, 2019-05-08)Current published protocols for targeted differentiation of human stem cells toward pancreatic β-cells fail to deliver sufficiently mature cells with functional properties comparable to human islet β-cells. We aimed to ... -
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example
(Peer reviewed; Journal article, 2008-07-02)Background: While the genomic annotations of diverse lineages of the Mycobacterium tuberculosis complex are available, divergences between gene prediction methods are still a challenge for unbiased protein dataset generation. ... -
Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics
(Peer reviewed; Journal article, 2014-01)With the advent of mass spectrometry based proteomics, the identification of thousands of proteins has become commonplace in biology nowadays. Increasingly, efforts have also been invested toward the detection and localization ... -
Proteomic analysis of formalin-fixed paraffin-embedded glomeruli suggests depletion of glomerular filtration barrier proteins in two-kidney one-clip hypertensive rats
(Peer reviewed; Journal article, 2014-08-16)Background It is well known that hypertension may cause glomerular damage, but the molecular mechanisms involved are still incompletely understood. Methods In the present study, we used formalin-fixed paraffin-embedded ... -
Proteomic analysis of neonatal meningitis-causing Escherichia coli
(Master thesis, 2017-11-30)Meningitis in newborns is a serious infection that causes mortality and neurological injury worldwide. The infection progresses from sepsis, and is dependent on the pathogen being able to cross the blood-brain barrier and ... -
Proteomic and histopathological characterisation of sicca subjects and primary Sjögren’s syndrome patients reveals promising tear, saliva and extracellular vesicle disease biomarkers
(Peer reviewed; Journal article, 2019-07-31)Background Mononuclear cell infiltration of exocrine glands, production of Ro/SSA and La/SSB autoantibodies, along with oral and ocular dryness, are characteristic features of primary Sjögren’s syndrome (pSS). Non-SS sicca ... -
Proteomic Profiling of Primary Human Acute Myeloid Leukemia Cells Does Not Reflect Their Constitutive Release of Soluble Mediators
(Peer reviewed; Journal article, 2018-12-20)Acute myeloid leukemia (AML) is a heterogeneous disease, and communication between leukemic cells and their neighboring leukemia-supporting normal cells is involved in leukemogenesis. The bone marrow cytokine network is ... -
Reliable FASP-based procedures for optimal quantitative proteomic and phosphoproteomic analysis on samples from acute myeloid leukemia patients
(Peer reviewed; Journal article, 2016-06-21)Background Satisfactory sample preparation for mass spectrometry-based analysis is a critical step in the proteomics workflow. The quality and reproducibility of sample preparation can determine the coverage and confidence ... -
thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer msf Files
(Peer reviewed; Journal article, 2011)The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has ... -
Tumor interstitial fluid formation, characterization, and clinical implications
(Peer reviewed; Journal article, 2015-05-26)The interstitium, situated between the blood and lymph vessels and the cells, consists of a solid or matrix phase and a fluid phase representing the tissue microenvironment. In the present review, we focus on the interstitial ... -
Urinary proteomics in chronic kidney disease: diagnosis and risk of progression beyond albuminuria
(Peer reviewed; Journal article, 2015-08-07)Background: The contrast between a high prevalence of chronic kidney disease (CKD) and the low incidence of end-stage renal disease highlights the need for new biomarkers of progression beyond albuminuria testing. Urinary ...