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https://www.readbyqxmd.com/read/28730086/peptidome-profiling-of-human-serum-of-uveal-melanoma-patients-based-on-magnetic-bead-fractionation-and-mass-spectrometry
#1
Xiang-Yu Shi, Qing Li, Wen-Bin Wei, Li-Ming Tao
AIM: To find new biomarkers for uveal melanoma (UM) by analyzing the serum peptidome profile. METHODS: Proteomic spectra in patients with UM before and after operation were analyzed and compared with those of healthy controls. Magnetic affinity beads were used to capture serum peptides and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer were used to compile serum peptide profiles. RESULTS: A panel of 49 peptides were differentially expressed between UM patients and controls, of which 33 peptides were of higher intensities in patient group and 16 peptides were of higher intensities in control group...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28711595/a%C3%AE-truncated-species-implications-for-brain-clearance-mechanisms-and-amyloid-plaque-deposition
#2
Erwin Cabrera, Paul Mathews, Emiliya Mezhericher, Thomas G Beach, Jingjing Deng, Thomas A Neubert, Agueda Rostagno, Jorge Ghiso
Extensive parenchymal and vascular Aβ deposits are pathological hallmarks of Alzheimer's disease (AD). Besides classic full-length peptides, biochemical analyses of brain deposits have revealed high degree of Aβ heterogeneity likely resulting from the action of multiple proteolytic enzymes. In spite of the numerous studies focusing in Aβ, the relevance of N- and C-terminal truncated species for AD pathogenesis remains largely understudied. In the present work, using novel antibodies specifically recognizing Aβ species N-terminally truncated at position 4 or C-terminally truncated at position 34, we provide a clear assessment of the differential topographic localization of these species in AD brains and transgenic models...
July 12, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28701697/peptidomics-of-an-in-vitro-digested-%C3%AE-gal-carrying-protein-revealed-ige-reactive-peptides
#3
D Apostolovic, M Krstic, J Mihailovic, M Starkhammar, T Cirkovic Velickovic, C Hamsten, M van Hage
The mammalian carbohydrate galactose-α1,3-galactose (α-Gal) causes a novel form of food allergy, red meat allergy, where patients experience severe allergic reactions several hours after red meat consumption. Here we explored gastric digestion of α-Gal glycoproteins using an in vitro model. Bovine thyroglobulin (BTG), a typical α-Gal carrying glycoprotein, was digested with pepsin. The resulting peptides were characterised by SDS PAGE, immunoblot and ImmunoCAP using sera from 20 red meat allergic patients...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28699258/cytotoxic-peptides-with-insulin-releasing-activities-from-skin-secretions-of-the-italian-stream-frog-rana-italica-ranidae
#4
J Michael Conlon, Vishal Musale, Samir Attoub, Maria Luisa Mangoni, Jérôme Leprince, Laurent Coquet, Thierry Jouenne, Yasser H A Abdel-Wahab, Peter R Flatt, Andrea C Rinaldi
Peptidomic analysis of norepinephrine-stimulated skin secretions from Italian stream frog Rana italica led to the purification and characterization of two host-defense peptides differing by a single amino acid residue belonging to the brevinin-1 family (brevinin-1ITa and -1ITb), a peptide belonging to the temporin family (temporin-ITa) and a component identified as prokineticin Bv8. The secretions contained relatively high concentrations of the methionine-sulphoxide forms of brevinin-1ITa and -1ITb suggesting that these peptides may have a role as antioxidants in the skin of this montane frog...
July 11, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28695291/missing-or-altered-self-human-nk-cell-receptors-that-recognize-hla-c
#5
REVIEW
Hugo G Hilton, Peter Parham
Natural killer (NK) cells are fast-acting and versatile lymphocytes that are critical effectors of innate immunity, adaptive immunity, and placental development. Controlling NK cell function are the interactions between killer-cell immunoglobulin-like receptors (KIRs) and their HLA-A, HLA-B and HLA-C ligands. Due to the extensive polymorphism of both KIR and HLA class I, these interactions are highly diversified and specific combinations correlate with protection or susceptibility to a range of infectious, autoimmune, and reproductive disorders...
July 10, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28677900/gastrointestinal-digestion-of-hazelnut-allergens-on-molecular-level-elucidation-of-degradation-kinetics-and-resistant-immunoactive-peptides-using-mass-spectrometry
#6
Robin Korte, Julia Bräcker, Jens Brockmeyer
SCOPE: Allergy to hazelnut seeds ranks among the most prevalent food allergies in Europe. The aim of this study was to elucidate the gastrointestinal digestion of hazelnut allergens on molecular level. METHODS AND RESULTS: Hazelnut flour was digested in vitro following the Infogest consensus model. For six allergenic proteins, the time-dependent course of digestion was monitored by SDS-PAGE and HPLC-MS/MS, and degradation products were characterized by a bottom-up proteomics approach...
July 5, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28674878/characterization-of-the-low-molecular-weight-human-plasma-peptidome
#7
David W Greening, Richard J Simpson
The human plasma proteome represents an important secreted sub-proteome. Proteomic analysis of blood plasma with mass spectrometry is a challenging task. The high complexity and wide dynamic range of proteins as well as the presence of several proteins at very high concentrations complicate the profiling of the human plasma proteome. The peptidome (or low-molecular-weight fraction, LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based markers of disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28658951/qualitative-and-quantitative-analysis-of-proteome-and-peptidome-of-human-follicular-fluid-using-multiple-samples-from-single-donor-with-lc-ms-and-swath-methodology
#8
Aleksandra Ewa Lewandowska, Katarzyna Macur, Paulina Czaplewska, Joanna Liss, Krzysztof Łukaszuk, Stanislaw Oldziej
Human follicular fluid (hFF) is a natural environment of oocyte maturation, and some components of hFF could be used to judge oocyte capability for fertilization and further development. In our pilot small scale study three samples from four donors (12 samples in total) were analyzed to determine which hFF proteins/peptides could be used to differentiate individual oocytes and which are patient specific. Ultrafiltration was used to fractionate hFF to High Molecular Weight (HMW) - proteome (>10kDa) and Low Molecular Weight (LMW) - peptidome (<10 kDa) fractions...
June 28, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28656816/annals-express-quantitative-measurement-of-a-candidate-serum-biomarker-peptide-derived-from-%C3%AE-2-hs-glycoprotein-and-a-preliminary-trial-of-multi-dimensional-peptide-analysis-in-females-with-pregnancy-induced-hypertension
#9
Kensuke Hamamura, Mitsuaki Yanagida, Hitoshi Ishikawa, Michio Banzai, Hiroshi Yoshitake, Daisuke Nonaka, Kenji Tanaka, Mayumi Sakuraba, Yasuka Miyakuni, Kenji Takamori, Michio Nojima, Koyo Yoshida, Hiroshi Fujiwara, Satoru Takeda, Yoshihiko Araki
PURPOSE: We previously attempted to develop quantitative enzyme-linked immunosorbent assay (ELISA) systems for the PDA039/044/071 peptides, potential serum disease biomarkers (DBMs) of pregnancy-induced hypertension (PIH), primarily identified by a peptidomic approach (BLOTCHIP(®)-mass spectrometry (MS)). However, our methodology did not extend to PDA071 (cysteinyl α2-HS-glycoprotein341-367), due to difficulty to produce a specific antibody against the peptide. The aim of the present study was to establish an alternative PDA071 quantitation system using liquid chromatography-multiple reaction monitoring (LC-MRM )/MS, to explore the potential utility of PDA071 as a DBM for PIH...
January 1, 2017: Annals of Clinical Biochemistry
https://www.readbyqxmd.com/read/28620443/pattern-recognition-for-predictive-preventive-and-personalized-medicine-in-cancer
#10
REVIEW
Tingting Cheng, Xianquan Zhan
Predictive, preventive, and personalized medicine (PPPM) is the hot spot and future direction in the field of cancer. Cancer is a complex, whole-body disease that involved multi-factors, multi-processes, and multi-consequences. A series of molecular alterations at different levels of genes (genome), RNAs (transcriptome), proteins (proteome), peptides (peptidome), metabolites (metabolome), and imaging characteristics (radiome) that resulted from exogenous and endogenous carcinogens are involved in tumorigenesis and mutually associate and function in a network system, thus determines the difficulty in the use of a single molecule as biomarker for personalized prediction, prevention, diagnosis, and treatment for cancer...
March 2017: EPMA Journal
https://www.readbyqxmd.com/read/28618245/multi-omics-integrative-investigation-of-fatty-acid-metabolism-in-obese-and-lean-subcutaneous-tissue
#11
Flavia Badoud, Dyanne Brewer, Armen Charchoglyan, Daniel J Cuthbertson, David M Mutch
White adipose tissue (WAT) plays a central role in whole-body energy homeostasis through storage and release of fatty acids. A deeper understanding of the complex and highly integrated pathways regulating WAT fatty acid metabolism, and how they are altered with obesity, is necessary for diagnostic and therapeutic innovations in nutritional disorders. In this multi-omics study, we investigated the influence of obesity on fatty acid metabolism in human subcutaneous adipose tissue (SAT) using an approach that integrated transcriptomic, peptidomic, and fatty acid analyses...
July 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28603764/data-on-endogenous-bovine-ovarian-follicular-cells-peptides-and-small-proteins-obtained-through-top-down-high-resolution-mass-spectrometry
#12
Valérie Labas, Ana-Paula Teixeira-Gomes, Laura Bouguereau, Audrey Gargaros, Lucie Spina, Aurélie Marestaing, Svetlana Uzbekova
The endogenous peptides and small proteins extracted from bovine ovarian follicular cells (oocytes, cumulus and granulosa cells) were identified by Top-down High Resolution Mass Spectrometry (TD-HR-MS/MS) in order to annotate peptido- and proteoforms detected using qualitative and quantitative profiling method based on ICM-MS (Intact Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry). The description and analysis of these Top-down MS data in the context of oocyte quality biomarkers research are available in the original research article of Labas et al...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28598000/peptidomic-analysis-of-maternal-serum-to-identify-biomarker-candidates-for-prenatal-diagnosis-of-tetralogy-of-fallot
#13
Bin Zhuang, Yin Hu, Xuemei Fan, Mengmeng Li, Jingai Zhu, Heng Liu, Li Cao, Dong Liang, Jingjing Zhang, Zhangbin Yu, Shuping Han
Tetralogy of Fallot (TOF) is the most common form of cyanotic congenital heart disease. To identify endogenous peptides possibly involved in the progression of TOF, we performed comparative peptidomic profiling of maternal serum between normal fetuses and fetuses suffering from TOF. A total of 278 differentially expressed peptides, including 94 over-expressed peptides and 184 under-expressed peptides, originating from 227 protein precursors were identified by Liquid Chromatography/Mass Spectrometry (LC/MS) in maternal serum of fetuses with TOF compared to normal controls...
June 9, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28594947/mass-spectrometry-based-serum-peptidome-profiling-accurately-and-reliably-predicts-outcomes-of-pemetrexed-plus-platinum-chemotherapy-in-patients-with-advanced-lung-adenocarcinoma
#14
Lin Wang, Chuanhao Tang, Bin Xu, Lin Yang, Lili Qu, Liangliang Li, Xiaoyan Li, Weixia Wang, Haifeng Qin, Hongjun Gao, Kun He, Xiaoqing Liu
BACKGROUND: Although pemetrexed plus cis/carboplatin has become the most effective chemotherapy regimen for patients with advanced lung adenocarcinoma, predictive biomarkers are not yet available, and new tools to identify chemosensitive patients who would likely benefit from this treatment are desperately needed. In this study, we constructed and validated predictive peptide models using the serum peptidome profiles of two datasets. METHODS: One hundred eighty-three patients treated with first-line platinum-based pemetrexed treatment for advanced lung adenocarcinoma were retrospectively enrolled and randomized into the training (n = 92) or validation (n = 91) set, and pre-treatment serum samples were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and ClinProTools software...
2017: PloS One
https://www.readbyqxmd.com/read/28588123/a-genoproteomic-approach-to-detect-peptide-markers-of-bacterial-respiratory-pathogens
#15
Honghui Wang, Steven K Drake, Chen Yong, Marjan Gucek, Matthew A Lyes, Avi Z Rosenberg, Erik Soderblom, M Arthur Moseley, John P Dekker, Anthony F Suffredini
BACKGROUND: Rapid identification of respiratory pathogens may facilitate targeted antimicrobial therapy. Direct identification of bacteria in bronchoalveolar lavage (BAL) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is confounded by interfering substances. We describe a method to identify unique peptide markers of 5 gram-negative bacteria by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for direct pathogen identification in BAL. METHODS: In silico translation and digestion were performed on 14-25 whole genomes representing strains of Acinetobacter baumannii, Moraxella catarrhalis, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Klebsiella pneumoniae...
June 6, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28566732/peptide-markers-for-rapid-detection-of-kpc-carbapenemase-by-lc-ms-ms
#16
Honghui Wang, Steven K Drake, Jung-Ho Youn, Avi Z Rosenberg, Yong Chen, Marjan Gucek, Anthony F Suffredini, John P Dekker
Carbapenemase producing organisms (CPOs) represent an urgent public health threat, and the need for new rapid methods to detect these organisms has been widely recognized. CPOs carrying the Klebsiella pneumoniae carbapenemase (bla KPC ) gene have caused outbreaks globally with substantial attributable mortality. Here we describe the validation of a rapid MS method for the direct detection of unique tryptic peptides of the KPC protein in clinical bacterial isolates with an isolate-to-result time of less than 90 minutes...
May 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28514659/the-intergenic-recombinant-hla-b%C3%A2-46-01-has-a-distinctive-peptidome-that-includes-kir2dl3-ligands
#17
Hugo G Hilton, Curtis P McMurtrey, Alex S Han, Zakia Djaoud, Lisbeth A Guethlein, Jeroen H Blokhuis, Jason L Pugh, Ana Goyos, Amir Horowitz, Rico Buchli, Ken W Jackson, Wilfred Bardet, David A Bushnell, Philip J Robinson, Juan L Mendoza, Michael E Birnbaum, Morten Nielsen, K Christopher Garcia, William H Hildebrand, Peter Parham
HLA-B(∗)46:01 was formed by an intergenic mini-conversion, between HLA-B(∗)15:01 and HLA-C(∗)01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B(∗)46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B(∗)46:01 has a low-diversity peptidome that is distinct from those of its parents...
May 16, 2017: Cell Reports
https://www.readbyqxmd.com/read/28490095/a-cold-induced-phytosulfokine-peptide-is-related-to-the-improvement-of-loquat-fruit-chilling-tolerance
#18
Huwei Song, Xinfeng Wang, Weicheng Hu, Xianghui Yang, Enjie Diao, Ting Shen, Qian Qiang
A novel peptidomics approach was used to discover cold-induced peptides in loquat fruit. Twenty unique peptides derived from 18 proproteins were identified, and they were involved in sugar signalling, protein metabolism and stress response. The quantitative analysis revealed 7 peptides with more than 2-fold upregulation, especially a 4.96-fold increase detected in the phytosulfokine (PSK) peptide. To further evaluate effects of PSK1 on fruit chilling tolerance, weight loss, firmness and internal browning were investigated in PSK1-treated loquat fruit at 0°C...
October 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28482090/p4p-a-peptidome-based-strain-level-genome-comparison-web-tool
#19
Aitor Blanco-Míguez, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez
Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting software existed to facilitate such phylogeny inference. Hence, we developed the Peptidomes for Phylogenies (P4P) web tool, which enables the survey of similarities between microbial proteomes and simplifies the process of obtaining new biological insights into their phylogeny...
May 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28474961/urine-peptidomic-biomarkers-for-diagnosis-of-patients-with-systematic-lupus-erythematosus
#20
M Pejchinovski, J Siwy, W Mullen, H Mischak, M A Petri, L C Burkly, R Wei
Background Systematic lupus erythematosus (SLE) is characterized with various complications which can cause serious organ damage in the human body. Despite the significant improvements in disease management of SLE patients, the non-invasive diagnosis is entirely missing. In this study, we used urinary peptidomic biomarkers for early diagnosis of disease onset to improve patient risk stratification, vital for effective drug treatment. Methods Urine samples from patients with SLE, lupus nephritis (LN) and healthy controls (HCs) were analyzed using capillary electrophoresis coupled to mass spectrometry (CE-MS) for state-of-the-art biomarker discovery...
January 1, 2017: Lupus
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