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Journal of Proteome Research

Christopher S Hughes, Victor Spicer, Oleg V Krokhin, Gregg B Morin
Methods for isobaric-tagged peptide analysis (e.g., TMT, iTRAQ), such as the synchronous precursor selection (SPS) tandem MS/MS/MS (MS(3)) approach, enable maintenance of reporter ion accuracy and precision by reducing the ratio compression caused by coisolated precursor ions. However, the decreased throughput of the MS(3) approach necessitates careful optimization of acquisition strategies and methods to ensure maximal proteome coverage. We present a systematic analysis of acquisition parameters used to analyze isobaric-tagged peptide samples on current generation Orbitrap mass spectrometer (MS) hardware...
April 20, 2017: Journal of Proteome Research
Christopher S Hughes, Chenchen Zhu, Victor Spicer, Oleg V Krokhin, Gregg B Morin
Multiplexed quantification with isobaric chemical tags (e.g., TMT, iTRAQ) provides a robust and efficient means to comparatively examine proteome dynamics between several biological states using a mass spectrometer (MS). The quantitative nature of isobaric tags necessitates strict validation of the observed ion signals in the chosen MS detector before differential patterns are extracted between biological states. We present an in-depth analysis of isobaric tag data acquired on current generation Orbitrap MS hardware to illustrate pitfalls in acquisition settings that can negatively impact results...
April 20, 2017: Journal of Proteome Research
Stefano Sala, Marleen Van Troys, Sandrine Medves, Marie Catillon, Evy Timmerman, An Staes, Elisabeth Schaffner-Reckinger, Kris Gevaert, Christophe Ampe
The multimodular nature of many eukaryotic proteins underlies their temporal or spatial engagement in a range of protein cocomplexes. Using the multimodule protein testin (TES), we here report a proteomics approach to increase insight in cocomplex diversity. The LIM-domain containing and tumor suppressor protein TES is present at different actin cytoskeleton adhesion structures in cells and influences cell migration, adhesion and spreading. TES module accessibility has been proposed to vary due to conformational switching and variants of TES lacking specific domains target to different subcellular locations...
April 20, 2017: Journal of Proteome Research
Timothy P Cleland, Caroline J DeHart, Ryan T Fellers, Alexandra J VanNispen, Joseph B Greer, Richard D LeDuc, W Ryan Parker, Paul M Thomas, Neil L Kelleher, Jennifer S Brodbelt
The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernible by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale...
April 19, 2017: Journal of Proteome Research
Nuwan R Vithanage, Thomas Richard Yeager, Jeevana Bhongir, Snehal R Jadhav, Chaminda Senaka Ranadheera, Enzo A Palombo, Nivedita Datta
Identification of psychrotrophic pathogenic and spoilage Gram-negative bacteria using rapid and reliable techniques is important in commercial milk processing, as these bacteria can produce heat-resistant proteases and act as post-processing contaminants in pasteurised milk. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a proven technology for identification of bacteria in food, however may require optimisation for identification of pathogenic and spoilage bacteria in milk and dairy products...
April 18, 2017: Journal of Proteome Research
Álvaro Sierra-Sánchez, Diego Garrido-Martín, Lucía Lourido, María González-González, Paula Díez, Cristina Ruiz-Romero, Ronald Sjöber, Conrad Droste, Javier De Las Rivas, Peter Nilsson, Francisco Blanco, Manuel Fuentes
Osteoarthritis (OA) is one of the most prevalent articular diseases. The identification of proteins closely associated with the diagnosis, progression, prognosis, and treatment response is dramatically required for this pathology. In this work, differential serum protein profiles have been identified in OA and rheumatoid arthritis (RA) by antibody arrays containing 151 antibodies against 121 antigens in a cohort of 36 samples. Then the identified differential serum protein profiles have been validated in a larger cohort of 282 samples...
April 17, 2017: Journal of Proteome Research
Xiaomeng Shen, Shichen Shen, Jun Li, Qiang Hu, Lei Nie, Chengjian Tu, Xue Wang, Benjamin Orsburn, Jianmin Wang, Jun Qu
In-depth and reproducible protein measurement in many biological samples is often critical for pharmaceutical/biomedical proteomics but remains challenging. MS1-based quantification using quadrupole/ultra-high-field Orbitrap(Q/UHF-Orbitrap) holds great promise, but the critically important experimental approaches enabling reliable large-cohort analysis have long been overlooked. Here we described an IonStar experimental strategy achieving excellent quantitative quality of MS1 quantification. Key features include: i)an optimized, surfactant-aided sample preparation approach provides highly efficient(>75%recovery) and reproducible(<15%CV) peptide recovery across large cell/tissue cohorts; ii)a long column with modest gradient length (e...
April 16, 2017: Journal of Proteome Research
Yeap S Ng, Alexandra Sorvina, Christie A Bader, Florian Weiland, Angel F Lopez, Peter Hoffmann, Tetyana Shandala, Douglas A Brooks
The evolutionary conserved family of 14-3-3 proteins appears to have a role in integrating numerous intracellular pathways, including signal transduction, intracellular trafficking, and metabolism. However, little is known about how this interactive network might be affected by the direct abrogation of 14-3-3 function. The loss of Drosophila 14-3-3ε resulted in reduced survival of mutants during larval-to-adult transition, which is known to depend on an energy supply coming from the histolysis of fat body tissue...
April 13, 2017: Journal of Proteome Research
Zhi Pi, Mei-Ling Zhao, Xian-Jun Peng, Shi-Hua Shen
Paper mulberry is a valuable woody species with a good chilling tolerance. In this study, phosphoproteomic analysis, physiological measurement, and mRNA quantification were employed to explore the molecular mechanism of chilling (4 °C) tolerance in paper mulberry. After chilling for 6 h, 427 significantly changed phosphoproteins were detected in paper mulberry seedlings without obvious physiological injury. When obvious physiological injury occurred after chilling for 48 h, a total of 611 phosphoproteins were found to be significantly changed at the phosphorylation level...
April 13, 2017: Journal of Proteome Research
Heike A Schmitt, Andreas Pich, Anke Schröder, Verena Scheper, Giorgio Lilli, Günter Reuter, Thomas Lenarz
The knowledge about the etiology and pathophysiology of sensorineural hearing loss (SNHL) is still very limited. This study aims at the improvement of understanding different types of SNHL by proteome analysis of human perilymph. Sampling of perilymph was established during inner ear surgeries (cochlear implantation, vestibular schwannoma surgeries), and safety of the sampling method was determined by checking hearing threshold with pure-tone audiometry postoperatively. An in-depth shot-gun proteomics approach was performed to identify cochlear proteins and the individual proteome in perilymph of patients...
April 13, 2017: Journal of Proteome Research
Laurie Favre, Annick Ortalo-Magné, Stéphane Greff, Thierry Pérez, Olivier P Thomas, Jean-Charles Martin, Gérald Culioli
Most marine bacteria can form biofilms, and they are the main components of biofilms observed on marine surfaces. Biofilms constitute a widespread life strategy, as growing in such structures offers many important biological benefits. The molecular compounds expressed in biofilms and, more generally, the metabolomes of marine bacteria remain poorly studied. In this context, a nontargeted LC-MS metabolomics approach of marine biofilm-forming bacterial strains was developed. Four marine bacteria, Persicivirga (Nonlabens) mediterranea TC4 and TC7, Pseudoalteromonas lipolytica TC8, and Shewanella sp...
April 12, 2017: Journal of Proteome Research
Meghan C Burke, Yuri A Mirokhin, Dmitrii V Tchekhovskoi, Sanford P Markey, Jenny Heidbrink Thompson, Christopher Larkin, Stephen E Stein
We present a mass spectral library-based method to identify tandem mass spectra of peptides that contain unanticipated modifications and amino acid variants. We describe this as a "hybrid" method because it combines matching both ion m/z and mass losses. The mass loss is the difference between the mass of an ion peak and the mass of its precursor. This difference, termed DeltaMass, is used to shift the product ions in the library spectrum that contain the modification, thereby allowing library product ions that contain the unexpected modification to match the query spectrum...
April 11, 2017: Journal of Proteome Research
Xuyun He, Ningning Zheng, Jiaojiao He, Can Liu, Jing Feng, Wei Jia, Houkai Li
The hypolipidemic effect of simvastatin varies greatly among patients. In the current study, we investigated the gut microbial-involved mechanisms underlying the different responses to simvastatin. Male C57BL/6J mice were divided into control (Con), high-fat/cholesterol diet (HFD), antibiotic (AB), simvastatin (SV) and antibiotic_simvastatin (AB_SV) groups, respectively. At the end of the experiment, serum samples were collected for lipids and metabolomic analysis, and liver tissues for histology, gene and protein expression analysis...
April 10, 2017: Journal of Proteome Research
Clifford Young, Alexandre V Podtelejnikov, Michael L Nielsen
Reversed phase chromatography is an established method for peptide separation and frequently coupled to electrospray ionization-mass spectrometry for proteomic analysis. Column temperature is one parameter that influences peptide retention and elution, but it is often overlooked as its implementation requires additional equipment and method optimization. An apparatus that allows temperature manipulation in three areas of a two-column setup was evaluated for improvements in chromatography. Using commercially available standards, we demonstrate that a low column temperature (0 °C) during sample loading enhances the peak shape of several bovine serum albumin hydrophilic peptides...
April 7, 2017: Journal of Proteome Research
Libang Yang, Zachery R Gregorich, Wenxuan Cai, Patrick Zhang, Bernice Young, Yiwen Gu, Jianyi Zhang, Ying Ge
Postinfarction remodeling and expansion of the peri-infarct border zone (BZ) directly correlate with mortality following myocardial infarction (MI); however, the cellular and molecular mechanisms underlying remodeling processes in the BZ remain unclear. Herein, we utilized a label-free quantitative proteomics approach in combination with immunohistochemical analyses to gain a better understanding of processes contributing to postinfarction remodeling of the peri-infarct BZ in a swine model of MI with reperfusion...
April 7, 2017: Journal of Proteome Research
Tobias Konz, Eugenia Migliavacca, Loïc Dayon, Gene L Bowman, Aikaterini Oikonomidi, Julius Popp, Serge Rezzi
We here describe the development, validation and application of a quantitative methodology for the simultaneous determination of 29 elements in human serum using state-of-the-art inductively coupled plasma triple quadrupole mass spectrometry (ICP-MS/MS). This new methodology offers high-throughput elemental profiling using simple dilution of minimal quantity of serum samples. We report the outcomes of the validation procedure including limits of detection/quantification, linearity of calibration curves, precision, recovery and measurement uncertainty...
April 6, 2017: Journal of Proteome Research
Yanyan Ma, Mingkun Yang, Xiaohuang Lin, Xin Liu, Hui Huang, Feng Ge
As a recently validated reversible post translational modification, lysine malonylation regulates diverse cellular processes from bacteria to mammals, but its existence and function in photosynthetic organisms remain unknown. Cyanobacteria are the most ancient group of photosynthetic prokaryotes and contribute about 50% of the total primary production on Earth. Previously, we reported the lysine acetylome in the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis). Here we performed the first proteomic survey of lysine malonylation in Synechocystis using highly accurate tandem mass spectrometry in combination with affinity purification...
April 6, 2017: Journal of Proteome Research
Aidan P Tay, Chi Nam Ignatius Pang, Daniel L Winter, Marc R Wilkins
Post-translational modifications of proteins (PTMs) act as key regulators of protein activity and of protein-protein interactions (PPIs). To date, it has been difficult to comprehensively explore functional links between PTMs and PPIs. To address this, we developed PTMOracle, a Cytoscape app for coanalyzing PTMs within PPI networks. PTMOracle also allows extensive data to be integrated and coanalyzed with PPI networks, allowing the role of domains, motifs, and disordered regions to be considered. For proteins of interest, or a whole proteome, PTMOracle can generate network visualizations to reveal complex PTM-associated relationships...
April 6, 2017: Journal of Proteome Research
Chao-Chao Du, Man-Jun Yang, Min-Yi Li, Jun Yang, Bo Peng, Hui Li, Xuan-Xian Peng
Crucial metabolites that modulate hosts' metabolome to eliminate bacterial pathogens have been documented, but the metabolic mechanisms are largely unknown. The present study explores the metabolic mechanism for l-leucine-induced metabolome to eliminate Streptococcus iniae in tilapia. GC-MS-based metabolomics was used to investigate the tilapia liver metabolic profile in the presence of exogenous l-leucine. Thirty-seven metabolites of differential abundance were determined, and 11 metabolic pathways were enriched...
April 5, 2017: Journal of Proteome Research
Srikrishnan Mallipeddi, Simion Kreimer, Nikolai Zvonok, V Kiran Vemuri, Barry L Karger, Alexander R Ivanov, Alexandros Makriyannis
Cannabinoid 2 receptor (CB2R), a Class A G-protein coupled receptor (GPCR), is a promising drug target in a wide array of pathological conditions. Rational drug design has been hindered due to our poor understanding of the structural features involved in ligand binding. Binding of a high-affinity biarylpyrazole inverse agonist AM1336 to a library of the human CB2 receptor (hCB2R) cysteine-substituted mutants provided indirect evidence that two cysteines in transmembrane helix-7 (H7) were critical for the covalent attachment...
April 4, 2017: Journal of Proteome Research
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