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MS and proteomics

Lara A Aqrawi, Xiangjun Chen, Janicke Liaaen Jensen, Mathias Kaurstad Morthen, Bernd Thiede, Øygunn Aass Utheim, Øyvind Palm, Behzod Tashbayev, Tor Paaske Utheim, Hilde Kanli Galtung
Ocular dryness is a characteristic feature of primary Sjögren's syndrome (pSS). This may result in dry eye disease (DED), leading to damage of the ocular surface. Additional, non-invasive diagnostic techniques are needed when evaluating pSS patients. Hence, screening for disease-specific biomarkers in biological fluid could be promising. We have previously examined the proteome of tear fluid from pSS patients through Liquid chromatography-mass spectrometry (LC-MS), and conducted a thorough ocular evaluation of patients with pSS...
2018: PloS One
Eduardo Anitua, María de la Fuente, Francisco Muruzabal, Ronald Mauricio Sánchez-Ávila, Jesús Merayo-Lloves, Mikel Azkargorta, Felix Elortza, Gorka Orive
PURPOSE: The main objective of this study is to compare the protein expression of human keratocytes treated with Plasma rich in growth factors (PRGF) or autologous serum (AS) and previously induced to myofibroblast by TGF-β1 treatment. METHODS: Blood from healthy donor was collected and processed to obtain AS and PRGF eye drops. Blood derivates were aliquoted and stored at -80°C until use. Keratocyte cells were pretreated for 60 minutes with 2.5 ng/ml TGF-β1...
2018: PloS One
Tao Liu, Jing Zhou, Hanjin Cui, Pengfei Li, Haigang Li, Yang Wang, Tao Tang
INTRODUCTION: Intracerebral hemorrhage (ICH) is a lethal cerebrovascular disorder with a high mortality and morbidity. The pathophysiological mechanisms underlying ICH-induced secondary injury remain unclear. METHODS: To examine one of the gaps in the knowledge about ICH pathological mechanisms, isobaric tag for relative and absolute quantification (iTRAQ)-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used in collagenase-induced ICH rats on the 2nd day...
October 11, 2018: Brain and Behavior
Agenor de Castro Moreira Dos Santos Júnior, Carlos André Ornelas Ricart, Arthur Henriques Pontes, Wagner Fontes, Agnelo Rodrigues de Souza, Mariana Souza Castro, Marcelo Valle de Sousa, Beatriz Dolabela de Lima
The protozoan Phytomonas serpens (class Kinetoplastea) is an important phytoparasite that has gained medical importance due to its similarities to Trypanosoma cruzi, the etiological agent of Chagas disease. The present work describes the first proteome analysis of P. serpens. The parasite was separated into cytosolic and high density organelle fractions, which, together with total cell extract, were subjected to LC-MS/MS analyses. Protein identification was conducted using a comprehensive database composed of genome sequences of other related kinetoplastids...
2018: PloS One
J Almeida, J Costa, P Coelho, V Cea, M Galesio, J P Noronha, M S Diniz, C Prudêncio, R Soares, C Sala, Rúben Fernandes
Gliomas represent the most common primary malignant brain tumors in adults, with an extremely poor prognosis. Among several risk factors, lifestyle was also recently identified as a major risk factor for the development of primary glioma. In the present study, we explore the relationship between obesity and glioma in a cellular model. Thus, we have study the influence of adipocytes secretome on glioma cell line GL261. Using the 3T3-L1 adipocyte cell line, and its conditioned medium (adipokines-enriched medium), we showed that adipocyte-released factors relate with glioma angiogenic, growth, hormones and metabolic behavior by MALDI-TOF-MS and proteomic array analysis...
October 9, 2018: Metabolic Brain Disease
Ye Xu, Yinghui Yuan, Nanshan Du, Yu Wang, Sheng Shu, Jin Sun, Shirong Guo
Various biotic and abiotic stresses threaten the cultivation of future agricultural crops. Among these stresses, heat stress is a major abiotic stress that substantially reduces agricultural productivity. Many strategies to enhance heat stress tolerance of crops have been developed, among which is grafting. Here, we show that Momordica-grafted cucumber scions have intrinsically enhanced chlorophyll content, leaf area, and net photosynthetic rate under heat stress compared to plants grafted onto cucumber rootstock...
2018: Horticulture Research
Somchai Chutipongtanate, Kenneth D Greis
The recent advance in targeted label-free proteomics, SWATH-MS, can provide consistent protein detection and reproducible protein quantitation, which is a considerable advantage for biomarker study of urinary extracellular vesicles. We developed a SWATH-MS workflow with a curated spectral library of 1,145 targets. Application of the workflow across nine replicates of three sample types (exosome-like vesicles (ELVs), microvesicles (MVs) and urine proteins (UPs)) resulted in the quantitation of 888 proteins at FDR <1%...
October 9, 2018: Scientific Reports
Hong Du, Honghao Liang, Yang Jiang, Xiaoxiao Qu, Haibo Yan, Xiaojuan Liu
Proteome response of plants is an important process that enables them to cope with environmental stress including metal stress. In this study, the proteome of Gracilaria lemaneiformis exposed to lead was investigated. Two-dimensional gel electrophoresis analysis revealed 123 protein spots, among which 14 proteins were significantly differentially expressed and identified using MALDI-TOF MS. Two of the up-regulated proteins were identified and predicted to be involved in photosynthesis and signal transduction, while eleven down-regulated proteins were functionally grouped into five classes including photosynthesis, energy metabolism, protein metabolism, carbohydrate transport and metabolism, and antioxidation proteins...
October 2018: Marine Pollution Bulletin
Baowei Chen, Linchuan Fang, Xueting Yan, Aiqian Zhang, Ping Chen, Tiangang Luan, Ligang Hu, Guibin Jiang
Metal contaminants present persistent and deleterious threats to environmental ecosystems and human health. Microorganisms can rapidly develop protective mechanisms against metal toxicity, such as metallothionein production. The identification of biological factors related to these protective mechanisms is essential for effective metal remediation. This study presents a robust pathway to rapidly locate and characterize a Pb-binding flagellin in Serratia Se1998, which can bind Pb at a 16:1 Pb: protein ratio...
October 3, 2018: Journal of Hazardous Materials
Yuanyuan Zhu, Lu Wu, Junjun Zhu, Yong Xu, Shiyuan Yu
To obtain a global insight into the dynamic protein expression pattern in Pichia stipitis during xylose fermentation in the presence of three representative inhibitors (acetic acid, vanillin, and 5-hydroxymethylfurfural), proteins were extracted for quantitative proteomic analysis using 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) on a liquid chromatography-mass/mass spectrometry (LC-MS/MS) instrument. Interestingly, aconitase (Aco1p) and NAD-isocitrate dehydrogenase (Idh1p), were upregulated during the middle exponential phase in the presence of the three inhibitors during tricarboxylic acid (TCA) cycle...
October 8, 2018: FEMS Microbiology Letters
Ng Yee Ling, Alfonso Olivos-García, Lim Teck Kwang, Rahmah Noordin, Lin Qingsong, Nurulhasanah Othman
Entamoeba histolytica is a protozoan parasite that causes amebiasis and poses a significant health risk for populations in endemic areas. The molecular mechanisms involved in the pathogenesis and regulation of the parasite are not well characterized. We aimed to identify and quantify the differentially abundant membrane proteins by comparing the membrane proteins of virulent and avirulent variants of E. histolytica HM-1:IMSS, and to investigate the potential associations among the differentially abundant membrane proteins...
October 8, 2018: American Journal of Tropical Medicine and Hygiene
Erin M Bertrand
Mass spectrometry-based proteomic approaches to studying microbial systems enable assessment of taxonomically resolved functional capacity. A subset of these proteomic approaches are absolutely quantitative, enabling comparisons of protein expression patterns between different studies and across environments. This chapter outlines a method for applying quantitative assays in marine microbial communities, using proteins involved in vitamin B12 (cobalamin) utilization and production as specific examples. This approach involves identifying important protein targets, determining taxonomic resolution of the required assays, identifying suitable peptides, developing and optimizing liquid chromatography-selected reaction monitoring mass spectrometry assays (LC-SRM-MS), and processing the resulting data...
2018: Methods in Molecular Biology
Ruixin Shao, Huifang Zheng, Jinliang Yang, Shuangjie Jia, Tianxue Liu, Yongchao Wang, Jiameng Guo, Qinghua Yang, Guozhang Kang
Nitric oxide (NO) is an important bioactive molecule that functions in regulating diverse abiotic stresses in plants, whereas its molecular mechanism remains obscure. In this study, treatment with 0.1 mM NO donor (sodium nitroprusside, SNP) significantly alleviated the inhibited growth induced by 15% polyethyleneglycol (PEG)-stimulated water deficiency (WD) for 3 days in maize seedlings, manifested by less decreased plant total fresh weight and dry weight. Comprehensive proteome analysis was further used to measure the expression profiles of leaf proteins of SNP-pretreated maize seedlings under WD conditions to explore the molecular mechanisms of NO-induced WD tolerance...
October 5, 2018: Nitric Oxide: Biology and Chemistry
Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Yoshinori Yamanouchi, Norie Araki, Akiyasu C Yoshizawa, Tsuyoshi Tabata, Mio Iwasaki, Naoyuki Sugiyama, Satoshi Tanaka, Susumu Goto, Yasushi Ishihama
Rapid progress is being made in mass spectrometry (MS)-based proteomics, yielding an increasing number of larger datasets with higher quality and higher throughput. To integrate proteomics datasets generated from various projects and institutions, we launched a project named jPOST (Japan ProteOme STandard Repository/Database, in 2015. Its proteomics data repository, jPOSTrepo, began operations in 2016 and has accepted more than 10 TB of MS-based proteomics datasets in the past two years...
October 8, 2018: Nucleic Acids Research
María Jesús Lerma-García, Maria Nicoletti, Ernesto Francisco Simó-Alfonso, Pier Giorgio Righetti, Elisa Fasoli
Combinatorial peptide ligand libraries (CPLLs), coupled to mass spectrometry, was applied to extensively map the proteome of apple fruits and to detect its presence in commercial apple juice and cider to evaluate their authenticity and genuineness. Using Uniprot_Malus database, 96 proteins were detected in apples, among which 30 proteins were specifically captured via CPLLs. Next, three proteins, previously recognized in fruits, were found in apple juice, which were involved in cellular metabolism of fruit maturation and in allergenic reactions...
October 8, 2018: Electrophoresis
Sun Young Lee, Seonjeong Lee, Sung Bum Park, Ki Young Kim, Jongki Hong, Dukjin Kang
We introduce a simple online 18 O-labeling protocol for protein samples that uses a parallelizing microbore hollow fiber enzyme reactor (mHFER) as an alternative tool for online proteolytic digestion. Online 18 O-labeling is performed by separately attaching two mHFERs in parallel to a 10-port switching valve with a high-pressure syringe pump and two syringes containing 16 O- or 18 O-water. 16 O-/18 O-labeled peptides are formed in this manner and simultaneously analyzed online using nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS) without any residual trypsin activity...
October 2, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Wendy E Heywood, Jenny Hallqvist, Amanda J Heslegrave, Henrik Zetterberg, Chiara Fenoglio, Elio Scarpini, Jonathan D Rohrer, Daniela Galimberti, Kevin Mills
There is an unmet need for markers that can stratify different forms and subtypes of dementia. Because of similarities in clinical presentation, it can be difficult to distinguish between Alzheimer's disease (AD) and frontotemporal dementia (FTD). Using a multiplex targeted proteomic LC-MS/MS platform, we aimed to identify cerebrospinal fluid proteins differentially expressed between patients with AD and FTD. Furthermore analysis of 2 confirmed FTD genetic subtypes carrying progranulin (GRN) and chromosome 9 open reading frame 72 (C9orf72) mutations was performed to give an insight into the differing pathologies of these forms of FTD...
August 25, 2018: Neurobiology of Aging
Isabella Piga, Stefano Casano, Andrew Smith, Silvia Tettamanti, Davide Leni, Giulia Capitoli, Angela Ida Pincelli, Marcella Scardilli, Stefania Galimberti, Fulvio Magni, Fabio Pagni
An accurate diagnostic classification of thyroid lesions remains an important clinical aspect that needs to be addressed in order to avoid "diagnostic" thyroidectomies. Among the several "omics" techniques, proteomics is playing a pivotal role in the search for diagnostic markers. In recent years, different approaches have been used, taking advantage of the technical improvements related to mass spectrometry that have occurred. Areas covered: The review provides an update of the recent findings in diagnostic classification, in genetic definition and in the investigation of thyroid lesions based on different proteomics approaches and on different type of specimens: cytological, surgical and biofluid samples...
October 5, 2018: Expert Review of Proteomics
Dennis Goldfarb, Michael J Lafferty, Laura E Herring, Wei Wang, Michael B Major
In mass spectrometry (MS)-based proteomics, protein and peptide sequences are determined by the isolation and subsequent fragmentation of precursor ions. When an isolation window captures only part of a precursor's isotopic distribution, the isotope distributions of the fragments depend on the subset of isolated precursor isotopes. Approximation of the expected isotope distributions of these fragments prior to sequence determination enables MS2 deisotoping, monoisotopic mass calculation, charge assignment of fragment peaks, and deconvolution of chimeric spectra...
September 30, 2018: ACS Omega
Loukia Roka, Konstantinos Koudounas, Gerasimos Daras, Jerome Zoidakis, Antonia Vlahou, Panagiotis Kalaitzis, Polydefkis Hatzopoulos
Olive is one of the most important fruit crop trees in the history of Mediterranean because of the high quality oil. Olive oil has a well-balanced fatty acid composition along with biophenols, which make it exceptional in human diet and provide an exceptional value to the olive oil. Leaf non-glandular peltate trichomes are specialized cell types representing a protective barrier against acute environmental conditions. To characterize the proteome of this highly differentiated cell type, we performed a comparative proteomic analysis among isolated trichomes and trichome-less leaves...
September 27, 2018: Journal of Plant Physiology
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