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MS and proteomics

Yiran Liang, Ying Zhu, Maowei Dou, Kerui Xu, Rosalie K Chu, William B Chrisler, Rui Zhao, Kimberly K Hixson, Ryan T Kelly
Due to sensitivity limitations, global proteome measurements generally require large amounts of biological starting material, which masks heterogeneity within the samples and differential protein expression among constituent cell types. Methods for spatially resolved proteomics are being developed to resolve protein expression for distinct cell types among highly heterogeneous tissues, but have primarily been applied to mammalian systems. Here we evaluate the performance of cell-type-specific proteome analysis of tomato fruit pericarp tissues by a platform integrating laser capture microdissection (LCM) and a recently developed automated sample preparation system (nanoPOTS, Nanodroplet Processing in One pot for Trace Samples)...
August 17, 2018: Analytical Chemistry
Christopher D Chouinard, Gabe Nagy, Ian K Webb, Tujin Shi, Erin Shammel Baker, Spencer A Prost, Tao Liu, Yehia M Ibrahim, Richard D Smith
Phosphoproteomics greatly augments proteomics and holds tremendous potential for insights into the modulation of biological systems for various disease states, etc. However, numerous challenges hinder conventional methods in terms of measurement sensitivity, throughput, quantification, and capabilities for confident phosphopeptide and phosphosite identification. In this work, we report the first example of integrating structures for lossless ion manipulations ion mobility-mass spectrometry (SLIM IM-MS) with online reversed-phase liquid chromatography (LC) to evaluate its potential for addressing the aforementioned challenges...
August 17, 2018: Analytical Chemistry
Jared B Shaw, Neha Malhan, Yury V Vasil'ev, Nathan I Lopez, Alexander A Makarov, Joseph S Beckman, Valery G Voinov
Compared to traditional collision induced dissociation methods, electron capture dissociation (ECD) provides more comprehensive characterization of large peptides and proteins and preserves labile post-translational modifications. However, ECD experiments are generally restricted to the high magnetic fields of FTICR-MS that enable simultaneous trapping of large polycations and electrons. Here, we demonstrate the use of an electromagnetostatic ECD cell to perform ECD and hybrid ECD methods utilizing 193 nm photons (ECuvPD) or collisional activation (EChcD) in a benchtop quadrupole-Orbitrap mass spectrometer...
August 17, 2018: Analytical Chemistry
Hans C Beck, Lisette O Jensen, Charlotte Gils, Albertine M M Ilondo, Martin Frydland, Christian Hassager, Ole K Møller-Helgestad, Jacob E Møller, Lars M Rasmussen
BACKGROUND: Several plasma proteins have been suggested as markers for a variety of cardiovascular conditions but fail to qualify in independent patient cohorts. This may relate to interference of medication on plasma protein concentrations. We used proteomics to identify plasma proteins that changed in concentration with heparin administration and therefore potentially may confound their evaluation as biomarkers in situations in which heparin is used. METHODS: We used a proteomic approach based on isobaric tagging and nano-LC-MS/MS analysis to quantify several hundred proteins in a discovery study in which individual plasma samples from 9 patients at intravascular ultrasound follow-up 12 months after an acute myocardial infarction before heparin administration and 2, 15, and 60 min after heparin administration; we validated our findings in 500 individual plasma samples obtained at admission from patients with suspected ST segment elevation myocardial infarction (STEMI), of whom 363 were treated with heparin before admission...
August 16, 2018: Clinical Chemistry
Hui-I Yu, Hsiu-Chuan Chou, Yi-Ching Su, Li-Hsun Lin, Chieh-Hsiang Lu, Hsiang-Hsun Chuang, Yi-Ting Tsai, En-Chi Liao, Yu-Shan Wei, Yi-Ting Yang, Ying-Ray Lee, Hong-Lin Chan
Evodiamine is a natural product extracted from herbal plants such as Tetradium which has shown to have anti-fat uptake and anti-proliferation properties. However, the effects of evodiamine on the behavior of thyroid cancers are largely unknown. To determine if evodiamine might be useful in the treatment of thyroid cancer and its cytotoxic mechanism, we analyzed the impact of evodiamine treatment on differential protein expression in human thyroid cancer cell line ARO using lysine-labeling two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry (MS)...
August 9, 2018: Journal of Pharmaceutical and Biomedical Analysis
Areeba Ahmad, Riaz Ahmad
We document the changes in sera and liver proteome during experimental hepatic fibrosis (HF) and its protection by resveratrol (Rsvtrl) in rats. HF was induced by N'-Nitrosodimethylamine (NDMA) administration thrice a week for 21-days. Compared to the control group, significant (P < 0.05) elevations in ALT, AST, ALP, γGT and bilirubin occurred during fibrosis. H&E, IHC for α-SMA and reticulin stainings of liver demonstrated that collagen amassing and HF were concurrent. Rsvtrl-supplementation refurbished hepatic architecture and lessened collagen deposition...
August 13, 2018: International Journal of Biological Macromolecules
Nellie A Martin, Arkadiusz Nawrocki, Viktor Molnar, Maria L Elkjaer, Eva K Thygesen, Miklos Palkovits, Peter Acs, Tobias Sejbaek, Helle H Nielsen, Zoltan Hegedus, Finn Sellebjerg, Tihamer Molnar, Eudes G V Barbosa, Nicolas Alcaraz, Ferenc Gallyas, Asa F Svenningsen, Jan Baumbach, Hans Lassmann, Martin R Larsen, Zsolt Illes
OBJECTIVE: Here, we applied a multi-omics approach (i) to examine molecular pathways related to de- and remyelination in multiple sclerosis (MS) lesions; and (ii) to translate these findings to the CSF proteome in order to identify molecules that are differentially expressed among MS subtypes. METHODS: To relate differentially expressed genes in MS lesions to de- and remyelination, we compared transcriptome of MS lesions to transcriptome of cuprizone (CPZ)-induced de- and remyelination...
2018: PloS One
The Trung Tran, Ravi Chand Bollineni, Christian Jeffrey Koehler, Bernd Thiede
Absolute targeted proteomics typically employs known amounts of synthetic stable isotopically labeled peptides which are mixed with the analyte and analysed by LC-MS to determine the concentration of proteins. In order to obtain more data, we evaluated the use of two different stable isotopes of the same peptide as spike-in for absolute quantification. For this purpose, peptide labeling by reductive amination was applied, which is a mild reaction for dimethylation of amine groups with very high yield. Three different forms can be generated with e...
August 16, 2018: Analyst
Xiangping Lin, Tao Liu, Pengfei Li, Zehui He, Yuanyuan Zhong, Hanjin Cui, Jiekun Luo, Yang Wang, Tao Tang
Background. Rhubarb, a traditional Chinese medicine, promotes viscera and remove blood stasis. Rhubarb is skilled in smoothening meridians, improving blood circulation which exhibits better efficacy on cerebral ischemic stroke. In this study, we aimed to analyze the underlying mechanisms of rhubarb which treated rats of middle cerebral artery occlusion (MCAO) model according to an iTRAQ-based proteomics and bioinformatics analysis. 30 rats were randomly allocated into three groups including sham group (SG), model group (MG), and rhubarb group (RG)...
2018: BioMed Research International
Nagihan Bostanci, Kai Bao, Li Xiaofei, Tomoki Maekawa, Jonas Grossmann, Christian Panse, Ruel A Briones, Ranillo R G Resuello, Joel V Tuplano, Cristina A G Garcia, Edimara S Reis, John D Lambris, George Hajishengallis
BACKGROUND AND AIM: Periodontitis is a prevalent chronic inflammatory disease associated with dysbiosis. Although complement inhibition has been successfully used to treat periodontitis in animal models, studies globally analysing inflamed tissue proteins to glean insight into possible mechanisms of action are missing. Using quantitative shotgun proteomics, we aimed to investigate differences in composition of inflammatory gingival tissue exudate ('gingival crevicular fluid'; GCF), before and after local administration of an inhibitor of the central complement component, C3, in non-human primates...
August 16, 2018: Journal of Proteome Research
Kristin H Jarman, Natalie C Heller, Sarah C Jenson, Janine R Hutchinson, Brooke L Deatherage Kaiser, Samuel H Payne, David S Wunschel, Eric D Merkley
Bottom-up proteomics is increasingly being used to characterize unknown environmental, clinical and forensic samples. Proteomics-based bacterial identification typically proceeds by tabulating peptide "hits" (i.e. confidently identified peptides) associated with the organisms in a database; those organisms with enough hits are declared present in the sample. This approach has proven successful in laboratory studies, however, important research gaps remain. First, the common-practice reliance on unique peptides for identification is susceptible to a phenomenon known as signal erosion...
August 15, 2018: Journal of Proteome Research
Hong-Xia Zhou, Richard I Milne, Xue-Long Ma, Yue-Qin Song, Jian-Yu Fang, Hang Sun, Hong-Guang Zha
Floral nectar plays important roles in the interaction between animal-pollinated plants and pollinators. Its components include water, sugars, amino acids, vitamins, and proteins. Growing empirical evidence shows that most of the proteins secreted in nectar (nectarines) are enzymes that can tailor nectar chemistry for their animal mutualists or reduce the growth of microorganisms in nectar. However, to date, the function of many nectarines remains unknown, and very few plant species have had their nectar proteome thoroughly investigated...
2018: Frontiers in Plant Science
Oren Avram, Anna Vaisman-Mentesh, Dror Yehezkel, Haim Ashkenazy, Tal Pupko, Yariv Wine
Reproducible and robust data on antibody repertoires are invaluable for basic and applied immunology. Next-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology, providing quantitative molecular information on antibody polyclonal composition. However, major computational challenges exist when analyzing antibody sequences, from error handling to hypermutation profiles and clonal expansion analyses. In this work, we developed the ASAP (A webserver for Immunoglobulin-Seq Analysis Pipeline) webserver (https://asap...
2018: Frontiers in Immunology
Janika Nättinen, Antti Jylhä, Ulla Aapola, Minna Parkkari, Alexandra Mikhailova, Roger W Beuerman, Hannu Uusitalo
Glaucoma patients are prone to concomitant ocular surface diseases; however, switching from preserved to preservative-free medication can often alleviate these symptoms. The objective of this study was to examine how the adverse effects and tear proteome change for glaucoma patients (n = 28) during a 12-month drug switch from preserved latanoprost (Xalatan) to preservative-free tafluprost (Taflotan). We hypothesized that patient stratification could help identify novel recovery patterns in both tear proteomics and clinical data...
August 13, 2018: Scientific Reports
Christina Ludwig, Ludovic Gillet, George Rosenberger, Sabine Amon, Ben C Collins, Ruedi Aebersold
Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH-MS is a specific variant of data-independent acquisition (DIA) methods and is emerging as a technology that combines deep proteome coverage capabilities with quantitative consistency and accuracy. In a SWATH-MS measurement, all ionized peptides of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion using rather large precursor isolation windows...
August 13, 2018: Molecular Systems Biology
Nicolai Bache, Philipp Emanuel Geyer, Dorte B Bekker-Jensen, Ole Hoerning, Lasse Falkenby, Peter V Treit, Sophia Doll, Igor Paron, Johannes Bruno Müller, Florian Meier, Jesper V Olsen, Ole Vorm, Matthias Mann
To further integrate mass spectrometry (MS)-based proteomics into biomedical research and especially into clinical settings, high throughput and robustness are essential requirements. They are largely met in high-flow rate chromatographic systems for small molecules but these are not sufficiently sensitive for proteomics applications. Here we describe a new concept that delivers on these requirements while maintaining the sensitivity of current nano-flow LC systems. Low-pressure pumps elute the sample from a disposable trap column, simultaneously forming a chromatographic gradient that is stored in a long storage loop...
August 13, 2018: Molecular & Cellular Proteomics: MCP
Yang Wu, Simon C Wagstaff, Saeed A Al-Harthi, Alister G Craig
BACKGROUND: To understand more about changes to the molecular components that occur when host endothelium interacts with Plasmodium falciparum-infected erythrocytes, a combined technique of protein separation (1D Blue-Native electrophoresis) and mass spectrometry of infected erythrocytes with endothelial cells (EC) in a co-culture system has been used. METHODS: Native proteins were extracted from co-cultures and identified by mass spectrometry. Proteomic data from different parasite strains, either adhesion proficient (to endothelial cells) or non-adherent, were analysed in parallel to reveal protein associations linked to cytoadherence...
August 13, 2018: Malaria Journal
Zhichang Yang, Xiaojing Shen, Daoyang Chen, Liangliang Sun
Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has been well recognized for bottom-up proteomics. It has approached 4000-8000 protein identifications (IDs) from a human cell line, mouse brains or Xenopus embryos via coupling with liquid chromatography (LC) prefractionation. However, at least five hundred micrograms of complex proteome digests were required for the LC-CZE-MS/MS studies. This requirement of a large amount of initial peptide material impedes the application of CZE-MS/MS for deep bottom-up proteomics of mass-limited samples...
August 13, 2018: Analytical Chemistry
Jianjun Li, Bie Tan, Yulong Tang, Peng Liao, Kang Yao, Peng Ji, Yulong Yin
This study aimed to explore the rule of degradation of dietary proteins by identifying chyme proteins in different segments of the digestive tract of growing pigs, using proteomics techniques. Six growing pigs were fed a corn-soybean meal-based diet for 7 days. The feedstuff and chyme proteins were separately extracted and separated with SDS-PAGE. 2D LCMS/MS combined with protein database searching identified 1,513 proteins in different segments of the gastrointestinal tract, the number of identified exogenous proteins gradually decline from the stomach to colon, with large amounts in the duodenum to the large intestine...
August 8, 2018: Science China. Life Sciences
Florian Gautier, Kateřina Eliášová, Jean-Charles Leplé, Zuzana Vondráková, Anne-Marie Lomenech, Claire Le Metté, Philippe Label, Guy Costa, Jean-François Trontin, Caroline Teyssier, Marie-Anne Lelu-Walter
BACKGROUND: To explore poorly understood differences between primary and subsequent somatic embryogenic lines of plants, we induced secondary (2ry ) and tertiary (3ry ) lines from cotyledonary somatic embryos (SEs) of two Douglas-fir genotypes: SD4 and TD17. The 2ry lines exhibited significantly higher embryogenic potential (SE yields) than the 1ry lines initiated from zygotic embryos (SD4, 2155 vs 477; TD17, 240 vs 29 g- 1 f.w.). Moreover, we observed similar differences in yield between 2ry and 3ry lines of SD4 (2400 vs 3921 g- 1 f...
August 10, 2018: BMC Plant Biology
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