journal
MENU ▼
Read by QxMD icon Read
search

Journal of Proteome Research

journal
https://www.readbyqxmd.com/read/28933156/we-are-not-alone-the-imop-initiative-and-its-roles-in-a-biology-and-disease-driven-human-proteome-project
#1
Andreas Tholey, Nicolas L Taylor, Joshua L Heazlewood, Emøke Bendixen
The Human Proteome is nearly fully mapped and will provide a knowledge base to accelerate our understanding of how proteins and protein networks can affect human health and disease. However, providing solutions to human health challenges will likely fail if insights are exclusively based on studies of human samples and human proteomes. In recent years, it has become evident that human health depends on an integrated understanding of the many species that make human life possible. These include the commensal microorganisms which are essential to human life, pathogens and food species as well as the classic model organisms that enable studies of biological mechanisms...
September 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28895742/human-prestin-a-candidate-pe1-protein-lacking-stringent-mass-spectrometric-evidence
#2
Abidali Mohamedali, Seong Beom Ahn, Varun K A Sreenivasan, Shoba Ranganathan, Mark S Baker
The evidence that any protein exists in the Human Proteome Project (HPP; protein evidence 1 or PE1) has revolved primarily (although not exclusively) around mass spectrometry (MS) (93% of PE1 proteins have MS evidence in the latest neXtProt release), with robust and stringent, well-curated metrics that have served the community well. This has led to a significant number of proteins still considered "missing" (i.e., PE2-4). Many PE2-4 proteins have MS evidence of unacceptable quality (small or not enough unitypic peptides and unacceptably high protein/peptide FDRs), transcriptomic, or antibody evidence...
September 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28929768/protein-corona-analysis-of-silver-nanoparticles-links-to-their-cellular-effects
#3
Sabine Juling, Alicia Niedzwiecka, Linda Böhmert, Dajana Lichtenstein, Soeren Selve, Albert Braeuning, Andreas F Thünemann, Eberhard Krause, Alfonso Lampen
The breadth of applications of nanoparticles and the access to food-associated consumer products containing nano-sized materials lead to oral human exposure to such particles. In biological fluids nanoparticles dynamically interact with biomolecules and form a protein corona. Knowledge about the protein corona is of great interest for understanding the molecular effects of particles as well as their fate inside the human body. We used a mass spectrometry-based toxicoproteomics approach to elucidate mechanisms of toxicity of silver nanoparticles and to comprehensively characterize the protein corona formed around silver nanoparticles in Caco-2 human intestinal epithelial cells...
September 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28929764/decoding-the-effect-of-isobaric-substitutions-on-identifying-missing-proteins-and-variant-peptides-in-human-proteome
#4
Wai-Kok Choong, Tung-Shing Mamie Lih, Yu-Ju Chen, Ting-Yi Sung
To confirm the existence of missing proteins, we need to identify at least two unique peptides with length of 9-40 amino acids of a missing protein in bottom-up mass spectrometry-based proteomic experiments. However, an identified unique peptide of the missing protein, even identified with high level of confidence, could possibly coincide with a peptide of a commonly observed protein due to isobaric substitutions, mass modifications, alternative splice isoforms, or single amino acid variants (SAAVs). Besides unique peptides of missing proteins, identified variant peptides (SAAV-containing peptides) could also alternatively map to peptides of other proteins due to the aforementioned issues...
September 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28927270/proteomic-analysis-of-peripheral-blood-mononuclear-cells-pbmc-after-a-high-fat-high-carbohydrate-meal-with-orange-juice
#5
Daniela F Seixas Chaves, Paulo C Carvalho, Elisa Brasili, Marcelo Macedo Rogero, Neuza Mariko Aymoto Hassimotto, Jolene K Diedrich, James J Moresco, John R Yates, Franco Maria Lajolo
Oxidative stress and inflammation play a role in the physiopathology of insulin resistance, diabetes and cardiovascular disease. A single high-fat, high-carbohydrate (HFHC) meal induces an increase in inflammatory and oxidative stress markers in peripheral blood mononuclear cells (PBMC). Previous studies have shown that orange juice is able to prevent this response by inhibiting toll like receptors (TLR) expression and endotoxemia. Our goal was to study the proteome response in PBMC after the consumption of a HFHC meal consumed with water, orange juice or an isocaloric beverage (water with glucose)...
September 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28927269/discovery-of-tamoxifen-and-n-desmethyl-tamoxifen-protein-targets-in-mcf-7-cells-using-large-scale-protein-folding-and-stability-measurements
#6
Ryenne N Ogburn, Lorrain Jin, He Meng, Michael C Fitzgerald
The proteins in an MCF-7 cell line were probed for tamoxifen (TAM) and n-desmethyl tamoxifen (NDT) induced stability changes using the Stability of Proteins from Rates of Oxidation (SPROX) technique in combination with two different quantitative proteomics strategies, including one based on SILAC and one based on isobaric mass tags. Over 1000 proteins were assayed for TAM- and NDT- induced protein stability changes, and a total of 163 and 200 protein hits were identified in the TAM and NDT studies, respectively...
September 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28925267/absolute-quantification-of-human-milk-caseins-and-the-whey-casein-ratio-during-the-first-year-of-lactation
#7
Yalin Liao, Darren Weber, Wei Xu, Blythe P Durbin-Johnson, Brett S Phinney, Bo Lönnerdal
Whey proteins and caseins in breast milk provide bioactivities and also have different amino acid composition. Accurate determination of these two major protein classes will therefore provide a better understanding of human milk composition and function, further aid in developing improved infant formulas based on bovine whey proteins and caseins. In this study, we implemented a LC-MS/MS quantitative analysis based on iBAQ label-free quantitation, to estimate absolute concentrations of alpha-casein, beta-casein and kappa-casein in human milk samples (n=88) collected between day 1 and day 360 post partum...
September 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28922609/serum-proteomic-variability-associated-with-clinical-phenotype-in-familial-transthyretin-amyloidosis-attrm
#8
Gloria G Chan, Clarissa M Koch, Lawreen H Connors
Transthyretin (TTR), normally a plasma circulating protein, can become misfolded and aggregated, ultimately leading to extracellular deposition of amyloid fibrils usually targeted to heart or nerve tissues. Referred to as TTR-associated amyloidoses (ATTR), this group of diseases is frequently life threatening and fatal if untreated. ATTR, caused by amyloid-forming variant TTR proteins (ATTRm) which arise from point mutations in the TTR gene, were classically referred to as familial amyloid cardiomyopathy (FAC) or familial amyloid polyneuropathy (FAP) reflecting the clinical phenotype...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28922600/ptml-model-for-proteome-mining-of-b-cell-epitopes-and-theoretic-experimental-study-of-bm86-protein-sequences-from-colima-mexico
#9
Saúl Gabriel Martínez, Esvieta Tenorio-Borroto, Alberto Barbabosa Pliego, Hector Diaz-Albiter, Juan C Vazquez-Chagoyan, Humbert Gonzalez-Diaz
In this work, we developed a general Perturbation Theory and Machine Learning (PTML) method for data mining of proteomes, in order to discover new B-cell epitopes useful for vaccine design. The method predicts the epitope activity εq(cqj) of one query peptide (q-peptide) in a set of experimental query conditions (cqj). The method uses as input the sequence of the q-peptide. The method also uses as input information about the sequence and epitope activity εr(crj) of a peptide of reference (r-peptide) assayed on similar experimental conditions (crj)...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28920697/n%C3%AE%C2%B5-and-o-acetylation-in-mycobacterium-tuberculosis-lineage-7-and-lineage-4-strains-proteins-involved-in-bioenergetics-virulence-and-antimicrobial-resistance-are-acetylated
#10
Alemayehu Godana Birhanu, Solomon Abebe Yimer, Carol Holm-Hansen, Gunnstein Norheim, Abraham Aseffa, Markos Abebe, Tone Tønjum
Increasing evidence demonstrates that lysine acetylation is involved in Mycobacterium tuberculosis (Mtb) virulence and pathogenesis. However, previous investigations in Mtb have only monitored acetylation at lysine residues using selected reference strains. We analyzed the global Nε- and O-acetylation of 3 Mtb isolates; 2 lineage 7 clinical isolates and the lineage 4 H37Rv reference strain. Quantitative acetylome analysis resulted in identification of 2490 class-I acetylation sites, among them 2349 O-acetylation and 141 Nε-acetylation sites, derived from 953 unique proteins...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28920441/new-insight-of-common-regulatory-pathways-in-human-trabecular-meshwork-cells-in-response-to-dexamethasone-and-prednisolone-using-an-integrated-quantitative-proteomics-swath-and-mrm-hr-mass-spectrometry
#11
Sze Wan Shan, Chi Wai Do, Thomas Chuen Lam, Ricky Pak Wing Kong, King Kit Li, Ka Man Chun, William Daniel Stamer, Chi Ho To
The molecular pathophysiology of corticosteroid-induced ocular hypertension (CIH) is not well understood. To determine the biological mechanisms of CIH, this study investigated protein expression profiles of human trabecular meshwork (hTM) cells in response to dexamethasone and prednisolone treatment. Both discovery-based Sequential Windowed data independent Acquisition of the Total High-resolution mass spectra (SWATH(TM)-MS) and targeted based high resolution multiple reaction monitoring (MRM-HR) confirmation were applied using a hybrid quadrupole-time-of-flight mass spectrometer...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28920440/unrestricted-mass-spectrometric-data-analysis-for-identification-localization-and-quantification-of-oxidative-protein-modifications
#12
Martin Rykær, Birte Svensson, Michael J Davies, Per Hägglund
Oxidation generates multiple diverse post-translational modifications resulting in changes in protein structure and function, associated with a wide range of diseases. Of these modifications, carbonylations have often been used as hallmarks of oxidative damage. However, accumulating evidence supports the hypothesis that other oxidation products may be quantitatively more important under physiological conditions. To address this issue we have developed a holistic mass spectrometry-based approach for simultaneous identification, localization and quantification of a broad range of oxidative modifications based on so-called 'dependent peptides'...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28862000/quantitative-proteomics-for-the-comprehensive-analysis-of-stress-responses-of-lactobacillus-paracasei-subsp-paracasei-f19
#13
Ann-Sophie Schott, Jürgen Behr, Andreas J Geißler, Bernhard Kuster, Hannes Hahne, Rudi F Vogel
Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress responses, discover general and specific markers for the investigated stress conditions, and predict optimal preconditioning for starter cultures, we performed a comprehensive genomic and quantitative proteomic analysis of a commonly used model system, Lactobacillus paracasei subsp...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28849940/metabolomic-fingerprinting-in-various-body-fluids-of-a-diet-controlled-clinical-smoking-cessation-study-using-a-validated-gc-tof-ms-metabolomics-platform
#14
Michael Goettel, Reinhard Niessner, Daniel Mueller, Max Scherer, Gerhard Scherer, Nikola Pluym
Untargeted GC-TOF-MS analysis proved to be a suitable analytical platform to determine alterations in the metabolic profile. Several metabolic pathways were found to be altered in a first clinical study comparing smokers against nonsmokers. Subsequently, we conducted a clinical diet-controlled study to investigate alterations in the metabolic profile during the course of 3 months of smoking cessation. Sixty male subjects were included in the study, and plasma, saliva, and urine samples were collected during four 24 h stationary visits: at baseline, while still smoking, after 1 week, after 1 month, and after 3 months of cessation...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28915052/mass-spectrometric-analysis-of-sox11-binding-proteins-in-head-and-neck-cancer-cells-demonstrates-the-interaction-of-sox11-and-hsp90%C3%AE
#15
Naseim Elzakra, Li Cui, Tong Liu, Hong Li, Junwei Huang, Shen Hu
Deregulated expression of SOX11 has been shown to involve in the progression of various types of cancer. However, the role of SOX11 in head and neck cancer remains largely unknown. In this study, co-immunoprecipitation (Co-IP) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were performed to identify the proteins that binds to SOX11 at significant higher levels in head and neck cancer cells compared to the normal human oral keratinocytes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that many potential SOX11-binding partners were associated with protein synthesis, cell metabolism and cell-cell adhesion...
September 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28914051/chromosome-centric-human-proteome-project-allies-with-developmental-biology-a-case-study-of-the-role-of-y-chromosome-genes-in-organ-development
#16
Anna Meyfour, Paria Pooyan, Sara Pahlavan, Mostafa Rezaei-Tavirani, Hamid Gourabi, Hossein Baharvand, Ghasem Hosseini Salekdeh
One of the main goals of Chromosome-Centric Human Proteome Project is to identify protein evidence for missing proteins (MPs). Here, we present a case study of the role of Y chromosome genes in organ development and how to overcome the challenges facing MPs identification by employing human pluripotent stem cell differentiation into cells of different organs yielding unprecedented biological insight into adult silenced proteins. Y chromosome is a male-specific sex chromosome which escapes meiotic recombination...
September 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28905631/ms-ms-free-protein-identification-in-complex-mixtures-using-multiple-enzymes-with-complementary-specificity
#17
Mark V Ivanov, Irina A Tarasova, Lev I Levitsky, Elizaveta M Solovyeva, Marina L Pridatchenko, Anna A Lobas, Julia A Bubis, Mikhail V Gorshkov
In this work, we present the results of evaluation of a workflow employing a multi-enzyme digestion strategy for MS1-based protein identification in "shotgun" proteomic applications. In the proposed strategy, several cleavage reagents of different specificity were used for parallel digestion of the protein sample followed by MS1 and retention time (RT) based search. Proof of principle for the proposed strategy was performed using experimental data obtained for the annotated 48-protein standard. Using the developed approach, up to 90% of proteins from the standard were unambiguously identified...
September 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28871782/antibiotic-treatment-preventing-necrotising-enterocolitis-alters-urinary-and-plasma-metabolomes-in-preterm-pigs
#18
Pingping Jiang, Alessia Trimigno, Jan Stanstrup, Bekzod Khakimov, Nanna Viereck, Søren Balling Engelsen, Per Torp Sangild, Lars Ove Dragsted
Necrotising enterocolitis (NEC) is a serious gut inflammatory condition in premature neonates, onset and development of which depend on the gut microbiome. Attenuation of the gut microbiome by antibiotics can reduce NEC incidence and severity. However, how the antibiotics-suppressed gut microbiome affects the whole-body metabolism in NEC-sensitive premature neonates is unknown. In formula-fed preterm pigs, used as a model for preterm infants, plasma and urinary metabolomes were investigated by LC-MS and (1)H NMR, with and without antibiotic treatment immediately after birth...
September 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28866885/targeted-proteomic-analyses-of-histone-h4-acetylation-changes-associated-with-homologous-recombination-deficient-high-grade-serous-ovarian-carcinomas
#19
Stefani N Thomas, Lijun Chen, Yang Liu, Naseruddin Höti, Hui Zhang
Approximately 20% of high-grade serous ovarian cancers are homologous-recombination (HR)-deficient due to genetic and epigenetic mutations of HR pathway genes including the tumor suppressor genes BRCA1 and 2. HR deficiency (HRD) compromises cells' ability to efficiently repair DNA damage, but it also increases sensitivity to chemotherapeutic treatment strategies; however, not all ovarian cancer patients with HRD tumors exhibit positive responses to chemotherapy. Our previous iTRAQ-based comprehensive proteomic characterization of high-grade serous ovarian carcinomas found that lower levels of histone H4 acetylation at Lys12 and Lys16 (H4-K12acK16ac) were associated with HRD tumors compared with non-HRD tumors...
September 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28849662/radiation-induced-endothelial-inflammation-is-transferred-via-the-secretome-to-recipient-cells-in-a-stat-mediated-process
#20
Jos Philipp, Omid Azimzadeh, Vikram Subramanian, Juliane Merl-Pham, Donna Lowe, Daniela Hladik, Nadine Erbeldinger, Svetlana Ktitareva, Claudia Fournier, Michael J Atkinson, Ken Raj, Soile Tapio
Radiation is the most common treatment of cancer. Minimizing the normal tissue injury, especially the damage to vascular endothelium, remains a challenge. This study aimed to analyze direct and indirect radiation effects on the endothelium by investigating mechanisms of signal transfer from irradiated to nonirradiated endothelial cells by means of secreted proteins. Human coronary artery endothelial cells (HCECest2) undergo radiation-induced senescence in vitro 14 days after exposure to 10 Gy X-rays. Proteomics analysis was performed on HCECest2 14 days after irradiation with X-ray doses of 0 Gy (control) or 10 Gy using label-free technology...
September 14, 2017: Journal of Proteome Research
journal
journal
39866
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"