keyword
MENU ▼
Read by QxMD icon Read
search

peptidomics

keyword
https://www.readbyqxmd.com/read/28079125/establishment-of-a-integrative-multi-omics-expression-database-ckddb-in-the-context-of-chronic-kidney-disease-ckd
#1
Marco Fernandes, Holger Husi
Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28063628/separate-effects-of-the-ankylosing-spondylitis-associated-erap1-and-erap2-aminopeptidases-determine-the-influence-of-their-combined-phenotype-on-the-hla-b-27-peptidome
#2
Adrian Martín-Esteban, Alejandro Sanz-Bravo, Pablo Guasp, Eilon Barnea, Arie Admon, José A López de Castro
Ankylosing spondylitis (AS) is an inflammatory disease strongly associated with the Major Histocompatibility Complex class I (MHC-I) allotype HLA-B*27. The endoplasmic reticulum aminopeptidases (ERAP)1 and 2, which trim peptides to their optimal length for MHC-I binding, are also susceptibility factors for this disease. Both highly active ERAP1 variants and ERAP2 expression favor AS, whereas loss-of-function ERAP1 and loss-of-expression ERAP2 variants are protective. Yet, only ERAP1 is in epistasis with HLA-B*27...
January 4, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28060824/chronological-profiling-of-plasma-native-peptides-after-hepatectomy-in-pigs-toward-the-discovery-of-human-biomarkers-for-liver-regeneration
#3
Kohta Iguchi, Etsuro Hatano, Takashi Nirasawa, Noriyuki Iwasaki, Motohiko Sato, Gen Yamamoto, Kenya Yamanaka, Tatsuya Okamoto, Yosuke Kasai, Naohiko Nakamura, Hiroaki Fuji, Tomohito Sakai, Nobuto Kakuda, Satoru Seo, Kojiro Taura, Kei Tashiro, Shinji Uemoto, Masaya Ikegawa
Liver regeneration after partial hepatectomy (PHx) is a time-dependent process, which is tightly regulated by multiple signaling cascades. Failure of this complex process leads to posthepatectomy liver failure (PHLF), which is associated with a high rate of mortality. Thus, it is extremely important to establish a useful biomarker of liver regeneration to help prevent PHLF. Here, we hypothesized that alterations in the plasma peptide profile may predict liver regeneration following PHx and hence we set up a diagnostic platform for monitoring posthepatectomy outcome...
2017: PloS One
https://www.readbyqxmd.com/read/28044435/expanding-the-cerebrospinal-fluid-endopeptidome
#4
Karl T Hansson, Tobias Skillbäck, Elin Pernevik, Silke Kern, Erik Portelius, Kina Höglund, Gunnar Brinkmalm, Jessica Holmén-Larsson, Kaj Blennow, Henrik Zetterberg, Johan Gobom
Biomarkers of neurodegenerative disorders are needed to assist in diagnosis, to monitor disease progression and therapeutic interventions, and to provide insight into disease mechanisms. One route to identify such biomarkers is by proteomic and peptidomic analysis of cerebrospinal fluid (CSF). In the current study, we performed an in-depth analysis of the human CSF endopeptidome to establish an inventory that may serve as a basis for future targeted biomarker studies. High-pH reversed-phase HPLC was employed for off-line sample prefractionation followed by low-pH nano-LC-MS analysis...
January 3, 2017: Proteomics
https://www.readbyqxmd.com/read/28033346/improving-phylogeny-reconstruction-at-the-strain-level-using-peptidome-datasets
#5
Aitor Blanco-Míguez, Jan P Meier-Kolthoff, Alberto Gutiérrez-Jácome, Markus Göker, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço
Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/28012108/differentiation-of-frogs-from-two-populations-belonging-to-the-pelophylax-esculentus-complex-by-lc-ms-ms-comparison-of-their-skin-peptidomes
#6
Tatiana Yu Samgina, Konstantin A Artemenko, Jonas Bergquist, Polonca Trebse, Gregor Torkar, Miriam D Tolpina, Albert T Lebedev
LC-MS/MS was applied to establish the composition of the skin peptidome of a Slovenian green frog belonging to the Pelophylax esculentus complex. As this was similar to the peptidome of the Moscow population of Pelophylax ridibundus, it allowed us to identify the Slovenian frog from the Pelophylax esculentus complex as Pelophylax ridibundus. The sequences of six new peptides from the brevinin 2 family are reported for the first time on the basis of manual interpretation of their tandem mass spectra. The structural similarity of the brevinin 2 peptides from the Moscow and Slovenian populations of Pelophylax ridibundus enables peptides from this family to be utilized as biomarkers for Pelophylax ridibundus inter- and intraspecies differentiation, and the proposed approach can be used as an analytical tool for differentiating the corresponding species and populations...
December 23, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28011936/the-mhc-class-ii-immunopeptidome-of-lymph-nodes-in-health-and-in-chemically-induced-colitis
#7
Tim Fugmann, Adriana Sofron, Danilo Ritz, Franziska Bootz, Dario Neri
We recently described a mass spectrometry-based methodology that enables the confident identification of hundreds of peptides bound to murine MHC class II (MHCII) molecules. In this article, we describe its application to the characterization of MHCII-bound peptides isolated from lymph nodes (LNs) of C57BL/6 mice. More than 1000 peptides could be identified in individual analyses, allowing a direct comparison of the MHCII peptidome in different types of normal LNs or in animals with colitis. The peptide length distribution and consensus sequences in axillary, brachial, inguinal, and mesenteric LNs were virtually identical, and a substantial portion of identified peptides corresponded to proteins found in all LNs...
December 23, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28000568/plant-peptides-bioactivity-opportunities-and-challenges
#8
Indira P Sarethy
Bioactive peptides from plants are an underexplored domain in the field of proteomics and peptidomics. Recent evidences of plant peptides being more than chemical signals and indeed, functioning in the responses of plants to diverse environmental cues such as stress and infection by pathogens, suggests their potentially wide applicability in agrochemical and pharmaceutical industries. With cutting-edge technologies available, studies on plant peptides still lag behind those from food or microorganisms. The current mini-review provides an overview of the major bioactivity documented of plant-based peptides...
December 20, 2016: Protein and Peptide Letters
https://www.readbyqxmd.com/read/27997202/peptigram-a-web-based-application-for-peptidomics-data-visualization
#9
Jean Manguy, Peter Jehl, Eugène T Dillon, Norman E Davey, Denis C Shields, Thérèse A Holton
Tandem mass spectrometry (MS/MS) techniques, developed for protein identification, are increasingly being applied in the field of peptidomics. Using this approach, the set of protein fragments observed in a sample of interest can be determined to gain insights into important biological processes such as signaling and other bioactivities. As the peptidomics era progresses, there is a need for robust and convenient methods to inspect and analyze MS/MS derived data. Here, we present Peptigram, a novel tool dedicated to the visualization and comparison of peptides detected by MS/MS...
December 20, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27983778/facile-synthesis-of-mesocrystalline-sno2-nanorods-on-reduced-graphene-oxide-sheets-an-appealing-multifunctional-affinity-probe-for-sequential-enrichment-of-endogenous-peptides-and-phosphopeptides
#10
Wen Ma, Feng Zhang, Liping Li, Shuai Chen, Limin Qi, Huwei Liu, Yu Bai
A novel multifunctional composite comprising mesocrystalline SnO2 nanorods (NRs) vertically aligned on reduced graphene oxide (rGO) sheets was synthesized and developed for sequential capture of endogenous peptides and phosphopeptides. With the hydrophobicity of rGO and high affinity of SnO2 nanorods, sequential enrichment of endogenous peptides and phosphopeptides could be easily achieved through a modulation of elution buffer. With this multifunctional nanomaterial, 36 peptides were observed from diluted bovine serum albumin (BSA) tryptic digest and 4 phosphopeptides could be selectively captured from β-casein digest...
December 28, 2016: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/27979737/in-vivo-digestomics-of-milk-proteins-in-human-milk-and-infant-formula-using-a-suckling-rat-pup-model
#11
Yasuaki Wada, Brett S Phinney, Darren Weber, Bo Lönnerdal
Human milk is the optimal mode of infant feeding for the first several months of life, and infant formulas serve as an alternative when breast-feeding is not possible. Milk proteins have a balanced amino acid composition and some of them provide beneficial bioactivities in their intact forms. They also encrypt a variety of bioactive peptides, possibly contributing to infant health and growth. However, there is limited knowledge of how milk proteins are digested in the gastrointestinal tract and bioactive peptides are released in infants...
December 13, 2016: Peptides
https://www.readbyqxmd.com/read/27933867/peptidomic-approach-to-developing-elisas-for-the-determination-of-bovine-and-porcine-processed-animal-proteins-in-feed-for-farmed-animals
#12
Anne-Catherine Huet, Caroline Charlier, Elise Deckers, Hélène Marbaix, Martine Raes, Sergio Mauro, Philippe Delahaut, Nathalie Gillard
The European Commission (EC) wants to reintroduce nonruminant processed animal proteins (PAPs) safely into the feed chain. This would involve replacing the current ban in feed with a species-to-species ban which, in the case of nonruminants, would only prohibit feeding them with proteins from the same species. To enforce such a provision, there is an urgent need for species-specific methods for detecting PAPs from several species in animal feed and in PAPs from other species. Currently, optical microscopy and the polymerase chain reaction are the officially accepted methods, but they have limitations, and alternative methods are needed...
November 30, 2016: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/27929071/methionine-sulfoxides-in-serum-proteins-as-potential-clinical-biomarkers-of-oxidative-stress
#13
Satoko Suzuki, Yoshio Kodera, Tatsuya Saito, Kazumi Fujimoto, Akari Momozono, Akinori Hayashi, Yuji Kamata, Masayoshi Shichiri
Oxidative stress contributes to the pathophysiology of a variety of diseases, and circulating biomarkers of its severity remains a topic of great interest for researchers. Our peptidomic strategy enables accurate and reproducible analysis of circulating proteins/peptides with or without post-translational modifications. Conventional wisdom holds that hydrophobic methionines exposed to an aqueous environment or experimental handling procedures are vulnerable to oxidation. However, we show that the mass spectra intensity ratio of oxidized to non-oxidized methionine residues in serum tryptic proteins can be accurately quantified using a single drop of human serum and give stable and reproducible results...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920218/a-molecular-basis-for-the-presentation-of-phosphorylated-peptides-by-hla-b-antigens
#14
Adán Alpízar, Fabio Marino, Antonio Ramos-Fernández, Manuel Lombardía, Anita Jeko, Florencio Pazos, Alberto Paradela, César Santiago, Albert J R Heck, Miguel Marcilla
As aberrant protein phosphorylation is a hallmark of tumor cells, the display of tumor-specific phosphopeptides by Human Leukocyte Antigen (HLA) class I molecules can be exploited in the treatment of cancer by T-cell-based immunotherapy. Yet, the characterization and prediction of HLA-I phospholigands is challenging as the molecular determinants of the presentation of such post-translationally modified peptides are not fully understood. Here, we employed a peptidomic workflow to identify 256 unique phosphorylated ligands associated with HLA-B*40, -B*27, -B*39 or -B*07...
December 5, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27914455/mediators-and-biomarkers-of-inflammation-in-meningitis-cytokine-and-peptidome-profiling-of-cerebrospinal-fluid
#15
A A Belogurov, O M Ivanova, Y A Lomakin, R H Ziganshin, M I Vaskina, V D Knorre, E A Klimova, A G Gabibov, V T Ivanov, V M Govorun
Differential diagnosis of bacterial and viral meningitis is an urgent problem of the modern clinical medicine. Early and accurate detection of meningitis etiology largely determines the strategy of its treatment and significantly increases the likelihood of a favorable outcome for the patient. In the present work, we analyzed the peptidome and cytokine profiles of cerebrospinal fluid (CSF) of 17 patients with meningitis of bacterial and viral etiology and of 20 neurologically healthy controls. In addition to the identified peptides (potential biomarkers), we found significant differences in the cytokine status of the CSF of the patients...
November 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27895531/follicular-fluid-biomarkers-for-human-in-vitro-fertilization-outcome-proof-of-principle
#16
Fang Chen, Carl Spiessens, Thomas D'Hooghe, Karen Peeraer, Sebastien Carpentier
BACKGROUND: Human follicular fluid (FF) is a unique biological fluid in which the oocyte develops in vivo, and presents an optimal source for non-invasive biochemical predictors. Oocyte quality directly influences the embryo development and hence, may be used as a predictor of embryo quality. Peptide profiling of FF and its potential use as a biomarker for oocyte quality has never been reported. METHODS: This study screened FF for peptide biomarkers that predict the outcome of in vitro fertilization (IVF)...
2016: Proteome Science
https://www.readbyqxmd.com/read/27873209/large-scale-interaction-profiling-of-protein-domains-through-proteomic-peptide-phage-display-using-custom-peptidomes
#17
Moon-Hyeong Seo, Satra Nim, Jouhyun Jeon, Philip M Kim
Protein-protein interactions are essential to cellular functions and signaling pathways. We recently combined bioinformatics and custom oligonucleotide arrays to construct custom-made peptide-phage libraries for screening peptide-protein interactions, an approach we call proteomic peptide-phage display (ProP-PD). In this chapter, we describe protocols for phage display for the identification of natural peptide binders for a given protein. We finally describe deep sequencing for the analysis of the proteomic peptide-phage display...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27863112/label-free-quantitative-comparison-of-cerebrospinal-fluid-glycoproteins-and-endogenous-peptides-in-subjects-with-alzheimer-s-disease-mild-cognitive-impairment-and-healthy-individuals
#18
Jingxin Wang, Robert Cunningham, Henrik Zetterberg, Sanjay Asthana, Cynthia Carlsson, Ozioma Okonkwo, Lingjun Li
PURPOSE: The goal of this study is to investigate putative molecular dynamic changes in cerebrospinal fluids (CSFs) collected from individuals with mild cognitive impairment (MCI) and Alzheimer's disease (AD) as compared to healthy controls. EXPERIMENTAL DESIGN: The CSF samples from 12 subjects comprised of four cognitively normal individuals and eight patients with MCI and AD, respectively. Two aliquots of each CSF samples (total 1 mL) of each participant are used for this study...
December 2016: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/27862975/purification-of-soluble-hla-class-i-complexes-from-human-serum-or-plasma-deliver-high-quality-immuno-peptidomes-required-for-biomarker-discovery
#19
Danilo Ritz, Andreas Gloger, Dario Neri, Tim Fugmann
Soluble human leukocyte antigen class I (sHLA)-peptide complexes have been suggested to play a role in the modulation of immune responses and in immune evasion of cancer cells. The set of peptides eluted from sHLA molecules could serve as biomarker for the monitoring of patients with cancer or other conditions. Here, we describe an improved sHLA peptidomics methodology resulting in the identification of 1816 to 2761 unique peptide sequences from triplicate analyses of serum or plasma taken from three healthy donors...
November 12, 2016: Proteomics
https://www.readbyqxmd.com/read/27861808/peptidomic-analysis-of-type-1-diabetes-associated-hla-dq-molecules-and-the-impact-of-hla-dm-on-peptide-repertoire-editing
#20
Zemin Zhou, Eduardo Reyes-Vargas, Hernando Escobar, Kuan Y Chang, Adam P Barker, Alan L Rockwood, Julio C Delgado, Xiao He, Peter E Jensen
HLA-DM and class II associated invariant chain (Ii) are key cofactors in the MHC class II (MHCII) antigen processing pathway. We used tandem mass spectrometry sequencing to directly interrogate the global impact of DM and Ii on the repertoire of MHCII-bound peptides in human embryonic kidney 293T cells expressing HLA-DQ molecules in the absence or presence of these cofactors. We found that Ii and DM have a major impact on the repertoire of peptides presented by DQ1 and DQ6, with the caveat that this technology is not quantitative...
November 15, 2016: European Journal of Immunology
keyword
keyword
114642
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"