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https://www.readbyqxmd.com/read/29776550/hydrophilic-probe-in-mesoporous-pore-for-selective-enrichment-of-endogenous-glycopeptides-in-biological-samples
#1
Yilin Li, Chunhui Deng, Nianrong Sun
As one of the most important post-translational modifications (PTMs) of peptidome, glycopeptidome is closely related to serious disease, especially to cancer. In order to specifically discover and analyze glycopeptidome biomarkers for clinical diagnosis of cancer on early-stage, it is crucial to develop efficient technique to analyze low-abundance of endogenous glycopeptides in biological samples. In this report, a hydrophilic probe in mesoporous pore (denoted as Fe3 O4 @mSiO2 @G6P) was designed and prepared...
September 18, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29774024/quantification-of-hla-dm-dependent-major-histocompatibility-complex-of-class-ii-immunopeptidomes-by-the-peptide-landscape-antigenic-epitope-alignment-utility
#2
Miguel Álvaro-Benito, Eliot Morrison, Esam T Abualrous, Benno Kuropka, Christian Freund
The major histocompatibility complex of class II (MHCII) immunopeptidome represents the repertoire of antigenic peptides with the potential to activate CD4+ T cells. An understanding of how the relative abundance of specific antigenic epitopes affects the outcome of T cell responses is an important aspect of adaptive immunity and offers a venue to more rationally tailor T cell activation in the context of disease. Recent advances in mass spectrometric instrumentation, computational power, labeling strategies, and software analysis have enabled an increasing number of stratified studies on HLA ligandomes, in the context of both basic and translational research...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29772785/comparison-of-human-milk-immunoglobulin-survival-during-gastric-digestion-between-preterm-and-term-infants
#3
Veronique Demers-Mathieu, Mark A Underwood, Robert L Beverly, Søren D Nielsen, David C Dallas
Human milk provides immunoglobulins (Igs) that supplement the passive immune system of neonates; however, the extent of survival of these Igs during gastric digestion and whether this differs between preterm and term infants remains unknown. Human milk, and infant gastric samples at 2 h post-ingestion were collected from 15 preterm (23⁻32 week gestational age (GA)) mother-infant pairs and from 8 term (38⁻40 week of GA) mother-infant pairs within 7⁻98 days postnatal age. Samples were analyzed via ELISA for concentration of total IgA (secretory IgA (SIgA)/IgA), total secretory component (SC/SIgA/SIgM), total IgM (SIgM/IgM), and IgG as well as peptidomics...
May 17, 2018: Nutrients
https://www.readbyqxmd.com/read/29769354/allele-specific-alterations-in-the-peptidome-underlie-the-joint-association-of-hla-a-29-02-and-endoplasmic-reticulum-aminopeptidase-2-erap2-with-birdshot-chorioretinopathy
#4
Alejandro Sanz-Bravo, Adrian Martin-Esteban, Jonas J W Kuiper, Marina García-Peydró, Eilon Barnea, Arie Admon, José A López de Castro
Virtually all patients of the rare inflammatory eye disease birdshot chorioretinopathy (BSCR) carry the HLA-A*29:02 allele. BSCR is also associated with endoplasmic reticulum aminopeptidase 2 (ERAP2), an enzyme involved in processing HLA class I ligands, thus implicating the A*29:02 peptidome in this disease. To investigate the relationship between both risk factors we employed label-free quantitative mass spectrometry to characterize the effects of ERAP2 on the A*29:02-bound peptidome. An ERAP2-negative cell line was transduced with lentiviral constructs containing GFP-ERAP2 or GFP alone, and the A*29:02 peptidomes from both transduced cells were compared...
May 16, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29763921/peptidomic-analysis-of-endometrial-tissue-from-patients-with-ovarian-endometriosis
#5
Yunping Xue, Pengfei Xu, Sujuan Xu, Kai Xue, Lingling Xu, Jie Chen, Juan Xu, Xiaoyan Shi, Qian Li, Lin Gu
BACKGROUND/AIMS: Ovarian endometriosis (OvE) is ovarian cyst that is lined with endometrial tissue. They are found in 17-44% of women with endometriosis. Their clinical manifestations include pelvic pain, dysmenorrhea, dyspareunia, and infertility. Although the incidence of OvE has increased yearly, the exact pathogenesis of OvE is still unclear. We used peptidomics, an emerging branch of proteomics, to identify differentially expressed peptides in order to determine the possible roles of these peptides in the pathogenesis of OvE...
May 9, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29761100/moving-the-cellular-peptidome-by-transporters
#6
REVIEW
Rupert Abele, Robert Tampé
Living matter is defined by metastability, implying a tightly balanced synthesis and turnover of cellular components. The first step of eukaryotic protein degradation via the ubiquitin-proteasome system (UPS) leads to peptides, which are subsequently degraded to single amino acids by an armada of proteases. A small fraction of peptides, however, escapes further cytosolic destruction and is transported by ATP-binding cassette (ABC) transporters into the endoplasmic reticulum (ER) and lysosomes. The ER-resident heterodimeric transporter associated with antigen processing (TAP) is a crucial component in adaptive immunity for the transport and loading of peptides onto major histocompatibility complex class I (MHC I) molecules...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29754444/peptidome-analysis-reveals-novel-serum-biomarkers-for-children-with-autism-spectrum-disorder-in-china
#7
Juan Yang, Yanni Chen, Xiaofan Xiong, Xiaobo Zhou, Lin Han, Ei Ni, Wenjing Wang, Xiaofei Wang, Lingyu Zhao, Dongdong Shao, Chen Huang
PURPOSE: Autism spectrum disorder (ASD) is a neurological and developmental disorder that begins early in childhood and lasts throughout one's life. Early diagnosis is essential for ASD since early treatment can enable children with ASD to make significant gains in language and social skills, but remains challenging since there are currently no specific biomarkers of ASD. The study aimed to identify serum biomarkers for ASD. EXPERIMENTAL DESIGN: Serum of Han Chinese children with ASD (n = 68) and age-matched healthy controls (n = 80) was analyzed using magnetic bead-based separation combined with mass spectrum...
May 13, 2018: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29741761/peptidome-analysis-of-lung-tissues-from-a-hyperoxia-induced-bronchopulmonary-dysplasia-mouse-model-insights-into-the-pathophysiological-process-of-bronchopulmonary-dysplasia
#8
Jing Yin, Xingyun Wang, Le Zhang, Xing Wang, Heng Liu, Yin Hu, Xiangyun Yan, Yongfeng Tang, Juan Wang, Zhengyin Li, Zhangbin Yu, Yan Cao, Shuping Han
The aim of this study was to identify and compare the peptidomic profiles of lung tissues from neonatal mice with and without bronchopulmonary dysplasia (BPD). Hyperoxia was used to establish the BPD mouse model. Lung tissues obtained on postnatal day (PND) 9 were processed for analysis via histological staining and label-free liquid chromatography-mass spectrometry (LC-MS/MS). Histological analysis of the lung sections from the BPD group showed significant alveolar simplification and aberrant pulmonary vascularization...
May 9, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29712860/the-c-terminal-extension-landscape-of-naturally-presented-hla-i-ligands
#9
Philippe Guillaume, Sarah Picaud, Petra Baumgaertner, Nicole Montandon, Julien Schmidt, Daniel E Speiser, George Coukos, Michal Bassani-Sternberg, Panagis Filippakopoulos, David Gfeller
HLA-I molecules play a central role in antigen presentation. They typically bind 9- to 12-mer peptides, and their canonical binding mode involves anchor residues at the second and last positions of their ligands. To investigate potential noncanonical binding modes, we collected in-depth and accurate HLA peptidomics datasets covering 54 HLA-I alleles and developed algorithms to analyze these data. Our results reveal frequent (442 unique peptides) and statistically significant C-terminal extensions for at least eight alleles, including the common HLA-A03:01, HLA-A31:01, and HLA-A68:01...
April 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29707912/cell-surface-mhc-class-i-expression-is-limited-by-the-availability-of-peptide-receptive-empty-molecules-rather-than-by-the-supply-of-peptide-ligands
#10
Liran Komov, Dganit Melamed Kadosh, Eilon Barnea, Elena Milner, Ayellet Hendler, Arie Admon
While antigen processing and presentation by the major histocompatibility complex class I molecules (MHC-I) have been extensively studied, a question arises as to whether the level of MHC-I expression is limited by the supply of peptide-receptive (empty) MHC molecules, or by the availability of peptide ligands for loading. To this end, we evaluated the MHC peptidomes resulting from exposure of human breast cancer cells (MCF-7) to interferons. Although all four HLA allotypes of the MCF-7 cells (HLA-A*02:01, B*18, B*44, and C*5) present peptides of similar lengths and C-termini, which should be processed similarly by the proteasome and by the antigen processing and presentation chaperones, the interferons induced differential modulation of the HLA-A, B and C peptidomes...
April 29, 2018: Proteomics
https://www.readbyqxmd.com/read/29701990/transcriptomic-and-neuropeptidomic-analysis-of-the-stick-insect-carausius-morosus
#11
Sander Liessem, Lapo Ragionieri, Susanne Neupert, Ansgar Buschges, Reinhard Predel
One of the most thoroughly studied insect species, with respect to locomotion behaviour, is the stick insect Carausius morosus. Although detailed information exists on premotor networks controlling walking, surprisingly little is known about neuropeptides, which are certainly involved in motor activity generation and modulation. So far, only few neuropeptides were identified from C. morosus or related stick insects. We performed a transcriptome analysis of the central nervous system to assemble and identify 65 neuropeptide and protein hormone precursors of C...
April 27, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29681522/epidemiologic-observations-guiding-clinical-application-of-a-urinary-peptidomic-marker-of-diastolic-left-ventricular-dysfunction
#12
Zhen-Yu Zhang, Esther Nkuipou-Kenfack, Wen-Yi Yang, Fang-Fei Wei, Nicholas Cauwenberghs, Lutgarde Thijs, Qi-Fang Huang, Ying-Mei Feng, Joost P Schanstra, Tatiana Kuznetsova, Jens-Uwe Voigt, Peter Verhamme, Harald Mischak, Jan A Staessen
Hypertension, obesity, and old age are major risk factors for left ventricular (LV) diastolic dysfunction (LVDD), but easily applicable screening tools for people at risk are lacking. We investigated whether HF1, a urinary biomarker consisting of 85 peptides, can predict over a 5-year time span mildly impaired diastolic LV function as assessed by echocardiography. In 645 white Flemish (50.5% women; 50.9 years [mean]), we measured HF1 by capillary electrophoresis coupled with mass spectrometry in 2005-2010. We measured early (E) and late (A) peak velocities of the transmitral blood flow and early (e') and late (a') mitral annular peak velocities and their ratios in 2009-2013...
March 21, 2018: Journal of the American Society of Hypertension: JASH
https://www.readbyqxmd.com/read/29667164/exploring-the-sea-urchin-neuropeptide-landscape-by-mass-spectrometry
#13
Eric B Monroe, Suresh P Annangudi, Andinet A Wadhams, Timothy A Richmond, Ning Yang, Bruce R Southey, Elena V Romanova, Liliane Schoofs, Geert Baggerman, Jonathan V Sweedler
Neuropeptides are essential cell-to-cell signaling messengers and serve important regulatory roles in animals. Although remarkable progress has been made in peptide identification across the Metazoa, for some phyla such as Echinodermata, limited neuropeptides are known and even fewer have been verified on the protein level. We employed peptidomic approaches using bioinformatics and mass spectrometry (MS) to experimentally confirm 23 prohormones and to characterize a new prohormone in nervous system tissue from Strongylocentrotus purpuratus, the purple sea urchin...
April 17, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29660150/sample-preparation-in-foodomic-analyses
#14
REVIEW
Tamara Martinović, Martina Šrajer Gajdošik, Djuro Josić
Representative sampling and adequate sample preparation are key factors for successful performance of further steps in foodomic analyses, as well as for correct data interpretation. Incorrect sampling and improper sample preparation can be sources of severe bias in foodomic analyses. It is well known that both wrong sampling and sample treatment cannot be corrected anymore. These, in the past frequently neglected facts, are now taken into consideration, and the progress in sampling and sample preparation in foodomics is reviewed here...
April 16, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29623661/editorial-and-review-29th-asms-sanibel-conference-on-mass-spectrometry-peptidomics-bridging-the-gap-between-proteomics-and-metabolomics-by-ms
#15
EDITORIAL
Lingjun Li, Per E Andrén, Jonathan V Sweedler
No abstract text is available yet for this article.
April 5, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29623538/optimization-for-peptide-sample-preparation-for-urine-peptidomics
#16
Tara K Sigdel, Carrie D Nicora, Wei-Jun Qian, Minnie M Sarwal
Analysis of native or endogenous peptides in biofluids can provide valuable insight into disease mechanisms. Furthermore, the detected peptides may also have utility as potential biomarkers for noninvasive monitoring of human diseases. The noninvasive nature of urine collection and the abundance of peptides in the urine make analysis by high-throughput "peptidomics" methods an attractive approach for investigating the pathogenesis of renal disease. However, urine peptidomics methodologies can be problematic with regard to difficulties associated with sample preparation...
April 6, 2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29611317/comparison-of-urine-and-plasma-peptidome-indicates-selectivity-in-renal-peptide-handling
#17
Pedro Magalhães, Claudia Pontillo, Martin Pejchinovski, Justyna Siwy, Magdalena Krochmal, Manousos Makridakis, Emma Carrick, Julie Klein, William Mullen, Joachim Jankowski, Antonia Vlahou, Harald Mischak, Joost P Schanstra, Petra Zürbig, Lars Pape
PURPOSE: Urine is considered to be produced predominantly as a result of plasma filtration in the kidney. However, the origin of the native peptides present in urine has never been investigated in detail. Therefore, we aimed to obtain a first insight into the origin of urinary peptides based on a side-by-side comprehensive analysis of the plasma and urine peptidome. METHODS: Twenty-two matched urine and plasma samples were analyzed for their peptidome using capillary electrophoresis coupled to mass spectrometry (CE-MS; for relative quantification) and CE- or LC coupled to tandem mass spectrometry (CE- or LC- MS/MS; for peptide identification)...
April 3, 2018: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29603653/an-analytical-method-for-assessing-optimal-storage-conditions-of-gingival-crevicular-fluid-and-disclosing-a-peptide-biomarker-signature-of-gingivitis-by-maldi-tof-ms
#18
Mariaimmacolata Preianò, Giuseppina Maggisano, Maria Stella Murfuni, Chiara Villella, Corrado Pelaia, Tiziana Montalcini, Nicola Lombardo, Girolamo Pelaia, Rocco Savino, Rosa Terracciano
PURPOSE: Gingival crevicular fluid (GCF) is an important diagnostic source of biomarkers for both periodontitis and gingivitis. However, GCF peptide signature may change depending on factors such as handling and storage. Here we propose a standardized methodology for GCF analysis by MALDI-TOF/TOF-MS in order to distinguish a characteristic peptide signature of gingivitis. EXPERIMENTAL DESIGN: The best storage/handling conditions which may ensure the stability of the endogenous peptidome in GCF is determined and then MALDI-TOF MS comparative analysis is performed...
March 30, 2018: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29602958/hla-g-peptide-preferences-change-in-transformed-cells-impact-on-the-binding-motif
#19
Alexander A Celik, Gwendolin S Simper, Wiebke Hiemisch, Rainer Blasczyk, Christina Bade-Döding
HLA-G is known for its strictly restricted tissue distribution. HLA-G expression could be detected in immune privileged organs and many tumor entities such as leukemia, multiple myeloma, and non-Hodgkin and Hodgkin's lymphoma. This functional variability from mediation of immune tolerance to facilitation of tumor immune evasion strategies might translate to a differential NK cell inhibition between immune-privileged organs and tumor cells. The biophysical invariability of the HLA-G heavy chain and its contrary diversity in immunity implicates a strong influence of the bound peptides on the pHLA-G structure...
March 30, 2018: Immunogenetics
https://www.readbyqxmd.com/read/29567172/saliva-as-a-source-of-new-phosphopeptide-biomarkers-development-of-a-comprehensive-analytical-method-based-on-shotgun-peptidomics
#20
Giorgia La Barbera, Anna Laura Capriotti, Chiara Cavaliere, Francesca Ferraris, Carmela Maria Montone, Susy Piovesana, Riccardo Zenezini Chiozzi, Aldo Laganà
The paper describes the development of an enrichment method for the analysis of the endogenous phosphopeptides in saliva. The method was based on magnetic solid phase extraction by a magnetic graphitized carbon black-TiO2 composite material and was developed considering different saliva pre-treatments, namely C18 solid phase extraction for purification, direct dilution in loading buffer or acetonitrile precipitation. The method was based on a shotgun proteomics workflow and the enriched peptide mixture was analysed by nanoHPLC and high resolution tandem mass spectrometry...
June 1, 2018: Talanta
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