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Proteomics biomarkers for solid tumors: Current status and future prospects

Published: Jun 11, 2018

Author(s): Iwona Belczacka, Agnieszka Latosinska, Jochen Metzger, David Marx, Antonia Vlahou, Harald Mischak, Maria Frantzi

Journal: Mass Spectrometry Reviews

Cancer is a heterogeneous multifactorial disease, which continues to be one of the main causes of death worldwide. Despite the extensive efforts for establishing accurate diagnostic assays and efficient therapeutic schemes, disease prevalence is on the rise, in part, however, also due to improved early detection. For years, studies were focused on genomics and transcriptomics, aiming at the discovery of new tests...

Read More thumbnail image: Proteomics biomarkers for solid tumors Current status and future prospects

Proteolysis to Identify Protease Substrates: Cleave to Decipher

Published: Jun 10, 2018

Author(s): Sonali R. Bhagwat, Krishnan Hajela, Amit Kumar

Journal: PROTEOMICS

Abstract Proteolysis is an irreversible post‐translational modification process, characterized by highly precise yet stable cleavage of proteins. Downstream events in signaling processes are reliant on proteolysis triggered by the protease activity. Studies indicate that abnormal proteolytic activity may lead to the manifestation of diseased conditions. Therefore, characterization of proteases may provide clues to understand their...

Read More thumbnail image: Proteolysis to Identify Protease Substrates Cleave to Decipher

Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline

Published: Jun 10, 2018

Author(s): Chao Du, Gilles P. Wezel

Journal: PROTEOMICS

Abstract Natural products (NPs) are a major source of compounds for medical, agricultural, and biotechnological industries. Many of these compounds are of microbial origin, and, in particular, from Actinobacteria or filamentous fungi. To successfully identify novel compounds that correlate to a bioactivity of interest, or discover new enzymes with desired functions, systematic multiomics approaches have been developed over the...

Read More thumbnail image: Mining for Microbial Gems Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline

Analysis of PNGase F‐Resistant N‐Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities

Published: Jun 10, 2018

Author(s): Johannes Stadlmann, David M. Hoi, Jasmin Taubenschmid, Karl Mechtler, Josef M. Penninger

Journal: PROTEOMICS

Abstract SugarQb ( www.imba.oeaw.ac.at/sugarqb) is a freely available collection of computational tools for the automated identification of intact glycopeptides from high‐resolution HCD MS/MS datasets in the Proteome Discoverer environment. We report the migration of SugarQb to the latest and free version of Proteome Discoverer 2.1, and apply it to the analysis of PNGase F‐resistant N‐glycopeptides from mouse embryonic stem cells. ...

Read More thumbnail image: Analysis of PNGase FResistant NGlycopeptides Using SugarQb for Proteome Discoverer 2_1 Reveals Cryptic Substrate Specificities

Utilizing two detectors in the measurement of trichloroacetic acid in human urine by reaction headspace gas chromatography

Published: Jun 8, 2018

Author(s): Wei‐Qi Xie, Yi‐Xian Gong, Kong‐Xian Yu

Journal: Biomedical Chromatography

Abstract A reaction headspace gas chromatography (HS‐GC) technique was investigated for quantitatively analyzing trichloroacetic acid in human urine. This method is based on the decomposition reaction of trichloroacetic acid under high‐temperature conditions. The carbon dioxide and chloroform formed from the decomposition reaction can be respectively detected by the thermal conductivity detection HS‐GC and flame ionization detection...

Read More thumbnail image: Utilizing two detectors in the measurement of trichloroacetic acid in human urine by reaction headspace gas chromatography

Pharmacokinetic and metabolism studies of bavachinin through ultra‐high‐performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry

Published: Jun 8, 2018

Author(s): Jun Qian, Fan Xie, Yanhong Shi, Jinhang Li, Liuqiang Zhang, Yiming Li, Fujiang Guo, Rui Wang

Journal: Biomedical Chromatography

Abstract Bavachinin (BVC), one of the main bioactive prenylated flavonoids derived from Psoralea corylifolia Linn, has a wide variety of pharmacological effects, such as antiangiogenic, antitumor, antiallergic, anti‐inflammatory and antibacterial activities, especially as a pan‐peroxisome proliferator‐activated receptors agonist. A rapid and sensitive method for quantifying BVC in rat plasma was developed and validated through...

Read More thumbnail image: Pharmacokinetic and metabolism studies of bavachinin through ultrahighperformance liquid chromatography coupled with electrospray ionization tandem mass spectrometry

Probing the dynamics of dithiooxamide coordinated to gold nanoparticles using SERS

Published: Jun 8, 2018

Author(s): Daniel Grasseschi, Vitor M. Zamarion, Henrique E. Toma

Journal: Journal of Raman Spectroscopy

Abstract The substitution kinetics and specific binding modes of the dithiooxamide (dto) ligand at the metal surface have been investigated and interpreted on the light of theoretical and experimental Raman studies. By monitoring the vibrational properties of this ligand, it was shown that gold nanoparticles employed as surface‐enhanced effects (SERS) probes are strongly dependent on the coordination chemistry of the ligands at the...

Read More thumbnail image: Probing the dynamics of dithiooxamide coordinated to gold nanoparticles using SERS

Development and applications of nonlinear optical spectroscopy: 16th ECONOS/36th ECW meeting in Jena (Germany)

Published: Jun 8, 2018

Author(s): Michael Schmitt, Jürgen Popp, Johannes Kiefer, Julian Moger

Journal: Journal of Raman Spectroscopy

Read More thumbnail image: Development and applications of nonlinear optical spectroscopy 16th ECONOS36th ECW meeting in Jena Germany

Polarization‐resolved Raman modes of monoclinic SrAl 2 O 4 ceramics

Published: Jun 8, 2018

Author(s): Anderson Dias, Roberto Luiz Moreira

Journal: Journal of Raman Spectroscopy

Abstract SrAl2O4 materials were obtained by molten salt synthesis and sintered at high temperatures to produce a ceramic body suitable for polarization‐resolved Raman spectroscopy measurements. Optimized experimental conditions were employed to study the complex vibrational spectrum of these ceramics under polarized light. A reliable set of experimental bands was obtained: 69 Raman modes were in fact observed, out of the 81 bands...

Read More thumbnail image: Polarizationresolved Raman modes of monoclinic SrAl 2 O 4 ceramics

Raman spectroscopy as a powerful technique for the identification of polymers used in cast sculptures from museum collections

Published: Jun 8, 2018

Author(s): Anna Klisińska‐Kopacz, Barbara Łydżba‐Kopczyńska, Monika Czarnecka, Tomasz Koźlecki, Julio Hoyo Mélendez, Agata Mendys, Anna Kłosowska‐Klechowska, Michał Obarzanowski, Piotr Frączek

Journal: Journal of Raman Spectroscopy

Abstract The chemical identification of materials is the first step for developing and implementing recommendations for the care and display of resin cast and plastic objects in museum collections. This paper presents advantages as well as limitations of portable Raman. Therefore, a comparative analysis of portable and benchtop Raman instruments was performed in the study of materials found in the contemporary art collections of the...

Read More thumbnail image: Raman spectroscopy as a powerful technique for the identification of polymers used in cast sculptures from museum collections

Metabolomic comparison between wild Ophiocordyceps sinensis and artificial cultured Cordyceps militaris

Published: Jun 7, 2018

Author(s): Lin Chen, Yuetao Liu, Qingfeng Guo, Qingxia Zheng, Wancun Zhang

Journal: Biomedical Chromatography

Abstract A systematic study on the metabolome differences between wild Ophiocordyceps sinensis and artificial cultured Cordyceps militaris was conducted using liquid chromatography−mass spectrometry. Principal component analysis and orthogonal projection on latent structure‐discriminant analysis results showed that C. militaris grown on solid rice medium (R‐CM) and C. militaris grown on tussah pupa (T‐CM) evidently separated and individually separated from...

Read More thumbnail image: Metabolomic comparison between wild Ophiocordyceps sinensis and artificial cultured Cordyceps militaris

Middle‐Down MS is Ready to Answer Complex Questions in Chromatin Biology

Published: Jun 7, 2018

Author(s): Simone Sidoli

Journal: PROTEOMICS

Abstract Histones are the most abundant protein family in the cells of complex organisms such as mammals and, together with DNA, they define the backbone of chromatin. Histone PTMs are key players of chromatin biology, as they function as anchors for proteins that bind and modulate chromatin readout, including gene expression. Middle‐down mass spectrometry (MS) has been optimized for about 10 years to study histone N‐terminal tails,...

Read More thumbnail image: MiddleDown MS is Ready to Answer Complex Questions in Chromatin Biology

Recent trends in sorption‐based sample preparation and liquid chromatography techniques for food analysis

Published: Jun 7, 2018

Author(s): Edvaldo V. Soares Maciel, Ana Lúcia Toffoli, Fernando Mauro Lanças

Journal: ELECTROPHORESIS

Abstract The accelerated rising of the world's population increased the consumption of food, thus demanding more rigors in the control of residue and contaminants in food–based products marketed for human consumption. In view of the complexity of most food matrices, including fruits, vegetables, different types of meat, beverages, among others, a sample preparation step is important to provide more reliable results when combined...

Read More thumbnail image: Recent trends in sorptionbased sample preparation and liquid chromatography techniques for food analysis

Preparative free‐flow electrophoresis, a versatile technology complementing gradient centrifugation in the isolation of highly purified cell organelles

Published: Jun 7, 2018

Author(s): Markus Islinger, Robert Wildgruber, Alfred Völkl

Journal: ELECTROPHORESIS

Abstract Free‐flow electrophoresis (FFE) exploits differences in the overall charge of bio‐particles separating cells, organelles, macromolecules, ions, etc. according to their distinct electrophoretic mobility and isoelectric point (pI) values. Indeed, around a neutral pH organelles usually exhibit a negative surface charge, migrating in an electric field from the cathode toward the anode. Since its introduction more than five decades ago by...

Read More thumbnail image: Preparative freeflow electrophoresis a versatile technology complementing gradient centrifugation in the isolation of highly purified cell organelles

Optimization of artemisinin extraction from Artemisia annua L. with supercritical carbon dioxide + ethanol using response surface methodology

Published: Jun 7, 2018

Author(s): Ozan Nazim Ciftci, Jessica Cahyadi, Selma E. Guigard, Marleny D. A. Saldaña

Journal: ELECTROPHORESIS

Abstract Malaria is a high priority life‐threatening public health concern in developing countries, and therefore there is a growing interest to obtain artemisinin for the production of artemisinin‐based combination therapy products. In this study, artemisinin was extracted from the Artemisia annua L. plant using supercritical carbon dioxide (SC‐CO2) modified with ethanol. Response surface methodology based on central composite rotatable design...

Read More thumbnail image: Optimization of artemisinin extraction from Artemisia annua L_ with supercritical carbon dioxide  ethanol using response surface methodology

A combined experimental and theoretical approach to determine X‐ray atomic fundamental quantities of tin

Published: Jun 7, 2018

Author(s): Y. Ménesguen, M.‐C. Lépy, J. M. Sampaio, J. P. Marques, F. Parente, M. Guerra, P. Indelicato, J. P. Santos, P. Hönicke, B. Beckhoff

Journal: X-Ray Spectrometry

The knowledge of atomic fundamental parameters, such as the mass attenuation coefficients or fluorescence yields with low uncertainties, is of decisive importance in elemental quantification involving X‐ray fluorescence analysis techniques. For example, several databases giving the mass attenuation coefficients are accessible and frequently used within a large community of users. These compilations are most often in good agreement for...

Read More thumbnail image: A combined experimental and theoretical approach to determine Xray atomic fundamental quantities of tin

Investigation of the pigment use in the Tomb of the Reliefs and other tombs in the Etruscan Banditaccia Necropolis

Published: Jun 7, 2018

Author(s): Matthias Alfeld, Cecilia Baraldi, Maria Cristina Gamberini, Philippe Walter

Journal: X-Ray Spectrometry

The pigment use in the Tomb of the Reliefs (fourth century BC) and four other tombs (seventh to fourth century BC) in the Etruscan Banditaccia Necropolis near Cerveteri, Italy, has been investigated. We made use of X‐ray fluorescence (XRF) and Raman spot analysis, XRF imaging, infrared luminescence and photography supported by Dstretch contrast enhancement. We identified the use of haematite, goethite, calcite, carbon black, manganese...

Read More thumbnail image: Investigation of the pigment use in the Tomb of the Reliefs and other tombs in the Etruscan Banditaccia Necropolis

Label‐free and non‐invasive BS‐SERS detection of liver cancer based on the solid device of silver nanofilm

Published: Jun 7, 2018

Author(s): Renming Liu, Yang Xiong, Yan Guo, Minzhen Si, Weiyue Tang

Journal: Journal of Raman Spectroscopy

Abstract Rapid and accurate diagnosis of cancers at early stage is clearly desirable, because it provides possibilities to cure the cancers in next treatments. Cancers at early stage usually occur and develop at a molecule level; however, it remains challenging for traditional methods to screen them timely. Here, the capability of using human blood serum surface‐enhanced Raman scattering (BS‐SERS) spectroscopy for label‐free,...

Read More thumbnail image: Labelfree and noninvasive BSSERS detection of liver cancer based on the solid device of silver nanofilm

Stable Protein Gel Storage in Acetonitrile for Mass Spectrometric Analysis

Published: Jun 6, 2018

Author(s): Yuxin Chen, Sen Wang, Jia Jia, Xinyu Tian, Hongpan Xu, Mingzhe Ning, Bing Bai

Journal: PROTEOMICS

Abstract Long‐term storage of protein samples for transportation is a challenge in the field of mass spectrometric analysis because the low temperature condition is not easy to be maintained. Here we introduce a simple method to preserve proteins at room temperature for at least one month. In this method, the protein sample is run shortly into a polyacrylamide gel which is then excised after Coomassie staining. The protein gel band...

Read More thumbnail image: Stable Protein Gel Storage in Acetonitrile for Mass Spectrometric Analysis

An Integrated Proteomic Approach Uncovers Novel Substrates and Functions of the Lon Protease in Escherichia coli

Published: Jun 6, 2018

Author(s): Jan Arends, Marcena Griego, Nikolas Thomanek, Claudia Lindemann, Blanka Kutscher, Helmut E. Meyer, Franz Narberhaus

Journal: PROTEOMICS

Abstract Controlling the cellular abundance and proper function of proteins by proteolysis is a universal process in all living organisms. In Escherichia coli, the ATP‐dependent Lon protease is crucial for protein quality control and regulatory processes. To understand how diverse substrates are selected and degraded, unbiased global approaches are needed. We employed a quantitative Super‐SILAC (stable isotope labeling with amino...

Read More thumbnail image: An Integrated Proteomic Approach Uncovers Novel Substrates and Functions of the Lon Protease in Escherichia coli
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