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proteomics analysis tools

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https://www.readbyqxmd.com/read/28727760/detection-of-titin-fragments-in-urine-in-response-to-exercise-induced-muscle-damage
#1
Kazue Kanda, Jun Sakuma, Takayuki Akimoto, Yasuo Kawakami, Katsuhiko Suzuki
Many studies have attempted to determine the associations between blood biomarkers and exercise-induced muscle damage. However, poor correlations between the changes in biomarker levels and the magnitude of muscle symptoms have been reported. Recent advances in proteomic tools offer a strategy for the comprehensive analysis of protein expression, which can be used to identify biomarkers. Here, we used a proteomic analysis to identify urinary proteins that appear in response to a calf-raise exercise, including repetitive eccentric muscle contractions, and found that a titin (also known as connectin) N-terminal fragment molecule appears in the urine after eccentric exercise...
2017: PloS One
https://www.readbyqxmd.com/read/28726736/protozoadb-2-0-a-trypanosoma-brucei-case-study
#2
Rodrigo Jardim, Diogo Tschoeke, Alberto M R Da Vila
Over the last decade new species of Protozoa have been sequenced and deposited in GenBank. Analyzing large amounts of genomic data, especially using Next Generation Sequencing (NGS), is not a trivial task, considering that researchers used to deal or focus their studies on few genes or gene families or even small genomes. To facilitate the information extraction process from genomic data, we developed a database system called ProtozoaDB that included five genomes of Protozoa in its first version. In the present study, we present a new version of ProtozoaDB called ProtozoaDB 2...
July 20, 2017: Pathogens
https://www.readbyqxmd.com/read/28724900/enhanced-differential-expression-statistics-for-data-independent-acquisition-proteomics
#3
Tomi Suomi, Laura L Elo
We describe a new reproducibility-optimization method ROPECA for statistical analysis of proteomics data with a specific focus on the emerging data-independent acquisition (DIA) mass spectrometry technology. ROPECA optimizes the reproducibility of statistical testing on peptide-level and aggregates the peptide-level changes to determine differential protein-level expression. Using a 'gold standard' spike-in data and a hybrid proteome benchmark data we show the competitive performance of ROPECA over conventional protein-based analysis as well as state-of-the-art peptide-based tools especially in DIA data with consistent peptide measurements...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724888/crosscheck-an-open-source-web-tool-for-high-throughput-screen-data-analysis
#4
Jamil Najafov, Ayaz Najafov
Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28722704/targeted-proteomic-assays-for-quantitation-of-proteins-identified-by-proteogenomic-analysis-of-ovarian-cancer
#5
Ehwang Song, Yuqian Gao, Chaochao Wu, Tujin Shi, Song Nie, Thomas L Fillmore, Athena A Schepmoes, Marina A Gritsenko, Wei-Jun Qian, Richard D Smith, Karin D Rodland, Tao Liu
Mass spectrometry (MS) based targeted proteomic methods such as selected reaction monitoring (SRM) are emerging as a promising tool for verification of candidate proteins in biological and biomedical applications. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute has investigated the standardization and analytical validation of the SRM assays and demonstrated robust analytical performance on different instruments across different laboratories. An Assay Portal has also been established by CPTAC to provide the research community a resource consisting of large sets of targeted MS-based assays, and a depository to share assays publicly...
July 19, 2017: Scientific Data
https://www.readbyqxmd.com/read/28722160/placental-proteomics-reveal-insights-into-fetal-alcohol-spectrum-disorders
#6
Katie L Davis-Anderson, Sebastian Berger, Emilie R Lunde-Young, Vishal D Naik, Heewon Seo, Greg A Johnson, Hanno Steen, Jayanth Ramadoss
Fetal alcohol spectrum disorders (FASD) describe many of the well-known neurodevelopmental deficits afflicting children exposed to alcohol in utero. The effects of alcohol on the maternal-fetal interface, especially the placenta, have been less explored. We herein hypothesized that chronic binge alcohol exposure during pregnancy significantly alters the placental protein profile in a rat FASD model METHODS: Pregnant rats were orogastrically treated daily with alcohol (4.5 g/kg, gestational day (GD) 5-10; 6...
July 19, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28718811/tissue-specific-labeling-in-proteomics
#7
REVIEW
Evelyn Ramberger, Gunnar Dittmar
Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed...
July 18, 2017: Proteomes
https://www.readbyqxmd.com/read/28716385/protein-lipograms
#8
Jason Laurie, Amit K Chattopadhyay, Darren R Flower
Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more letters. A protein lipogram likewise omits one or more types of amino acid. In this article, we establish a usable terminology for the decomposition of a sequence collection in terms of the lipogram. Next, we characterize Uniref50 using a lipogram decomposition. At the global level, protein lipograms exhibit power-law properties...
July 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28711385/top-down-proteomics-for-the-analysis-of-proteolytic-events-methods-applications-and-perspectives
#9
REVIEW
Andreas Tholey, Alexander Becker
Mass spectrometry based proteomics is an indispensable tool for almost all research areas relevant for the understanding of proteolytic processing, ranging from the identification of substrates, products and cleavage sites up to the analysis of structural features influencing protease activity. The majority of methods for these studies are based on bottom-up proteomics performing analysis at peptide level. As this approach is characterized by a number of pitfalls, e.g. loss of molecular information, there is an ongoing effort to establish top-down proteomics, performing separation and MS analysis both at intact protein level...
July 12, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28702376/nematode-species-identification-current-status-challenges-and-future-perspectives-for-cyathostomins
#10
Christina M Bredtmann, Jürgen Krücken, Jayaseelan Murugaiyan, Tetiana Kuzmina, Georg von Samson-Himmelstjerna
Human and animal health is globally affected by a variety of parasitic helminths. The impact of co-infections and development of anthelmintic resistance requires improved diagnostic tools, especially for parasitic nematodes e.g., to identify resistant species or attribute pathological effects to individual species or particular species combinations. In horses, co-infection with cyathostomins is rather a rule than an exception with typically 5 to 15 species (out of more than 40 described) per individual host...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28702021/combination-of-metabolomic-and-proteomic-analysis-revealed-different-features-among-lactobacillus-delbrueckii-subspecies-bulgaricus-and-lactis-strains-while-in-vivo-testing-in-the-model-organism-caenorhabditis-elegans-highlighted-probiotic-properties
#11
Elena Zanni, Emily Schifano, Sara Motta, Fabio Sciubba, Claudio Palleschi, Pierluigi Mauri, Giuditta Perozzi, Daniela Uccelletti, Chiara Devirgiliis, Alfredo Miccheli
Lactobacillus delbrueckii represents a technologically relevant member of lactic acid bacteria, since the two subspecies bulgaricus and lactis are widely associated with fermented dairy products. In the present work, we report the characterization of two commercial strains belonging to L. delbrueckii subspecies bulgaricus, lactis and a novel strain previously isolated from a traditional fermented fresh cheese. A phenomic approach was performed by combining metabolomic and proteomic analysis of the three strains, which were subsequently supplemented as food source to the model organism Caenorhabditis elegans, with the final aim to evaluate their possible probiotic effects...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28701906/proteomic-discovery-and-verification-of-serum-amyloid-a-as-a-predictor-marker-of-patients-at-risk-of-post-stroke-infection-a-pilot-study
#12
L Azurmendi, V Lapierre-Fetaud, J Schneider, J Montaner, M Katan, Jean-Charles Sanchez
BACKGROUND: Post-stroke infections occur in 20-36% of stroke patients and are associated with high morbidity and mortality rates. Early identification of patients at risk of developing an infection could improve care via an earlier treatment leading to a better outcome. We used proteomic tools in order to discover biomarkers able to stratify patients at risk of post-stroke infection. METHODS: The post hoc analysis of a prospective cohort study including 40 ischemic stroke patients included 21 infected and 19 non-infected participants...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28695509/proteome-wide-identification-of-in-vivo-adp-ribose-acceptor-sites-by-liquid-chromatography-tandem-mass-spectrometry
#13
Sara C Larsen, Mario Leutert, Vera Bilan, Rita Martello, Stephanie Jungmichel, Clifford Young, Michael O Hottiger, Michael L Nielsen
ADP-ribosylation is a posttranslational modification (PTM) that affects a variety of cellular processes. In recent years, mass spectrometry (MS)-based proteomics has become a valuable tool for studying ADP-ribosylation. However, studying this PTM in vivo in an unbiased and sensitive manner has remained a difficult challenge. Here, we describe a detailed protocol for unbiased analysis of ADP-ribosylated proteins and their ADP-ribose acceptor sites under physiological conditions. The method relies on the enrichment of mono-ADP-ribosylated peptides using the macrodomain Af1521 in combination with liquid chromatography-high-resolution tandem MS (LC-MS/MS)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28690680/from-grass-to-gas-microbiome-dynamics-of-grass-biomass-acidification-under-mesophilic-and-thermophilic-temperatures
#14
Christian Abendroth, Claudia Simeonov, Juli Peretó, Oreto Antúnez, Raquel Gavidia, Olaf Luschnig, Manuel Porcar
BACKGROUND: Separating acidification and methanogenic steps in anaerobic digestion processes can help to optimize the process and contribute to producing valuable sub-products such as methane, hydrogen and organic acids. However, the full potential of this technology has not been fully explored yet. To assess the underlying fermentation process in more detail, a combination of high-throughput sequencing and proteomics on the acidification step of plant material (grass) at both mesophilic and thermophilic temperatures (37 and 55 °C, respectively) was applied for the first time...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28689516/an-update-on-medium-and-low-abundant-blood-plasma-proteome-of-horse
#15
A Lepczyński, M Ożgo, A Dratwa-Chałupnik, P Robak, A Pyć, D Zaborski, A Herosimczyk
The main objectives of the study were to: (1) deeply analyse the serum protein composition of Equus caballus, (2) assess the effectiveness of the high-abundant protein depletion and improve the concentration of medium- and low-abundant proteins. The analysis were performed on the blood plasma of three healthy part-Arabian mares. The implementation of two-dimensional electrophoresis and matrix-assisted laser desorption/ionisation - time of flight mass spectrometry allowed us to establish a horse plasma proteome map...
July 10, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28688084/chemical-proteomic-analysis-of-6-benzylaminopurine-molecular-partners-in-wheat-grains
#16
Radim Simerský, Ivo Chamrád, Jindřich Kania, Miroslav Strnad, Marek Šebela, René Lenobel
An affinity-based chemical proteomic technique enabled direct identification of BAP-interacting proteins in wheat, including the well-known cytokinin-binder, cytokinin-binding protein 1. In this work, we show the development of a chemical proteomic technique for the identification of proteins binding to natural aromatic cytokinins (CKs). 6-benzylaminopurine (BAP) and documented CK-binder, wheat germ-allocated cytokinin-binding protein 1 (CBP-1), were suggested as an ideal proof-of concept affinity pair. Therefore, wheat grains were chosen as a model plant material...
July 7, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28686798/multiplierz-v2-0-a-python-based-ecosystem-for-shared-access-and-analysis-of-native-mass-spectrometry-data
#17
William M Alexander, Scott B Ficarro, Guillaume Adelmant, Jarrod A Marto
The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data...
July 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28684183/proteomic-approaches-to-decipher-cancer-cell-secretome
#18
REVIEW
Jessica Brandi, Marcello Manfredi, Giulia Speziali, Fabio Gosetti, Emilio Marengo, Daniela Cecconi
In this review, we give an overview of the actual proteomic approaches used in the study of cancer cells secretome. In particular, we describe the proteomic strategies to decipher cancer cell secretome initially focusing on the different aspects of sample preparation. We examine the issues related to the presence of low abundant proteins, the analysis of secreted proteins in the conditioned media with or without the removal of fetal bovine serum and strategies developed to reduce intracellular protein contamination...
July 3, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28683725/maldi-tof-ms-analysis-in-discovery-and-identification-of-serum-proteomic-patterns-of-ovarian-cancer
#19
Agata Swiatly, Agnieszka Horala, Joanna Hajduk, Jan Matysiak, Ewa Nowak-Markwitz, Zenon J Kokot
BACKGROUND: Due to high mortality and lack of efficient screening, new tools for ovarian cancer (OC) diagnosis are urgently needed. To broaden the knowledge on the pathological processes that occur during ovarian cancer tumorigenesis, protein-peptide profiling was proposed. METHODS: Serum proteomic patterns in samples from OC patients were obtained using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Eighty nine serum samples (44 ovarian cancer and 45 healthy controls) were pretreated using solid-phase extraction method...
July 6, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28674883/proteomic-analysis-of-blood-extracellular-vesicles-in-cardiovascular-disease-by-lc-ms-ms-analysis
#20
Montserrat Baldan-Martin, Fernando de la Cuesta, Gloria Alvarez-Llamas, Gema Ruiz-Hurtado, Luis M Ruilope, Maria G Barderas
Extracellular vesicles are membrane vesicles related to cell communication. These vesicles consist of proteins, RNA, and microRNA and are an interesting and important tool to understand the processes taking place in the secreting cell, especially in diseases in which its release is often enhanced. The used of blood extracellular vesicles in cardiovascular disease as a low invasive, easily accessible source of circulating markers could give us important information related to pathological process even more with the use of proteomic analysis...
2017: Methods in Molecular Biology
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