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Journal of Proteomics

Barbara Deracinois, Luc Camoin, Matthias Lambert, Jean-Baptiste Boyer, Erwan Dupont, Bruno Bastide, Caroline Cieniewski-Bernard
The O-linked-N-acetyl-d-glucosaminylation (O-GlcNAcylation) modulates numerous aspects of cellular processes. Akin to phosphorylation, O-GlcNAcylation is highly dynamic, reversible, and responds rapidly to extracellular demand. Despite the absolute necessity to determine post-translational sites to fully understand the role of O-GlcNAcylation, it remains a high challenge for the major reason that unmodified proteins are in excess comparing to the O-GlcNAcylated ones. Based on a click chemistry approach, O-GlcNAcylated proteins were labelled with azido-GalNAc and coupled to agarose beads...
July 14, 2018: Journal of Proteomics
Katharine A Horzmann, Leeah S Reidenbach, Devang H Thanki, Anna E Winchester, Brad A Qualizza, Geoffrey A Ryan, Kaitlyn E Egan, Victoria E Hedrick, Tiago J P Sobreira, Samuel M Peterson, Gregory J Weber, Sara E Wirbisky-Hershberger, Maria S Sepúlveda, Jennifer L Freeman
Atrazine (ATZ), the second most commonly used herbicide in the United States, is an endocrine disrupting chemical linked to cancer and a common drinking water contaminant. This study further investigates ATZ-related developmental toxicity by testing the following hypotheses in zebrafish: the effects of embryonic ATZ exposure are dependent on timing of exposure; embryonic ATZ exposure alters brain development and function; and embryonic ATZ exposure changes protein abundance in carcinogenesis-related pathways...
July 13, 2018: Journal of Proteomics
Xinpei Yi, Bo Wang, Zhiwu An, Fuzhou Gong, Jing Li, Yan Fu
Study of single amino acid variations (SAVs) of proteins, resulting from single nucleotide polymorphisms, is of great importance for understanding the relationships between genotype and phenotype. In mass spectrometry based shotgun proteomics, identification of peptides with SAVs often suffers from high error rates on the variant sites detected. These site errors are due to multiple reasons and can be confirmed by manual inspection or genomic sequencing. Here, we present a software tool, named SAVControl, for site-level quality control of variant peptide identifications...
July 13, 2018: Journal of Proteomics
Bruno Méhul, Agnes Perrin, Karine Grisendi, Antonio Núñez Galindo, Loïc Dayon, Corinne Ménigot, Yves Rival, Johannes J Voegel
Histone deacetylases (HDACs) are key enzymes involved in epigenetic modulation and were targeted by HDAC inhibitors (HDACis) for cancer treatment. The action of HDACis is not restricted to histones and also prevents deacetylation of other proteins, supporting their wide biological actions. The HuT78 cell line is recognized as a key tool to support and understand cutaneous T-cell lymphoma (CTCL) biology and was used as a predictive model since HDACi such as Vorinostat and Panobinostat have both demonstrated apoptotic activities in HuT78 cells and in primary blood CTCL cells...
July 13, 2018: Journal of Proteomics
Julia Bespyatykh, Alexander Smolyakov, Andrei Guliaev, Egor Shitikov, Georgij Arapidi, Ivan Butenko, Marine Dogonadze, Olga Manicheva, Elena Ilina, Victor Zgoda, Vadim Govorun
Nowadays proteomics is one of the major instruments for editing and correcting annotation of genomic information. The correct genome annotation is necessary for omics studies of clinically relevant pathogens like Mycobacterium tuberculosis as well as for the progress in drug design and in silico biology. Here, we focused on the proteogenomic analysis of W-148 strain belonging to the Beijing B0/W148 cluster. This cluster, also known as a "successful" clone possesses unique pathogenic properties and has a unique genome organization...
July 13, 2018: Journal of Proteomics
Venkatanaidu Karri, David Ramos, Julia Bauzá Martinez, Antonia Odena, Eliandre Oliveira, Susan L Coort, Chris T Evelo, Edwin C M Mariman, Marta Schuhmacher, Vikas Kumar
Chronic exposure to heavy metals such as Pb, As, and MeHg can be associated with an increased risk of developing neurodegenerative diseases. Our in vitro bioassays results showed the potency of heavy metals in the order of Pb < As < MeHg on hippocampal cells. The main objective of this study was combining in vitro label free proteomics and systems biology approach for elucidating patterns of biological response, discovering underlying mechanisms of Pb, As, and MeHg toxicity in hippocampal cells...
July 11, 2018: Journal of Proteomics
Geng-Rui Zhu, Xing Yan, Dong Zhu, Xiong Deng, Ji-Su Wu, Jian Xia, Yue-Ming Yan
Lysine acetylation is a widespread protein posttranslational modification in all organisms. However, quantitative acetylproteome characterization in response to water deficit during crop grain development remains unknown. In the study, we performed the first large-scale acetylproteome analysis of developing wheat grains under water-deficit using label-free quantitative proteome approach. In total, 716 acetylated sites corresponding to 442 acetylated proteins were identified, of which 106 acetylated sites representing 93 acetylated proteins (including 88 non-histones) showed significant changes under water-deficit...
July 9, 2018: Journal of Proteomics
Radfan Ahmed, Santosh Kodgire, B Santhakumari, Rajendra Patil, Mahesh Kulkarni, Gajanan Zore
To understand the impact of fetal bovine serum (FBS) on metabolism and cellular architecture in addition to morphogenesis, we have identified FBS responsive proteome of Candida albicans. FBS induced 34% hyphae and 60% pseudohyphae in C. albicans at 30 °C while 98% hyphae at 37 °C. LC-MS/MS analysis revealed that 285 proteins modulated significantly in response to FBS at 30 °C and 37 °C. Out of which 152 were upregulated and 62 were downregulated at 30 °C while 18 were up and 53 were downregulated at 37 °C...
June 26, 2018: Journal of Proteomics
Jia You, Athit Kao, Roslyn Dillon, Lisa J Croner, Ryan Benz, John E Blume, Bruce Wilcox
Over the past 20 years, mass spectrometry (MS) has emerged as a dynamic tool for proteomics biomarker discovery. However, published MS biomarker candidates often do not translate to the clinic, failing during attempts at independent replication. The cause can be shortcomings in study design, sample quality, assay quantitation, and/or quality/process control. To address these shortcomings, we developed an MS workflow in accordance with Tier 2 measurement requirements for targeted peptides, defined by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) "fit-for-purpose" approach, using dynamic multiple reaction monitoring (dMRM) which measures specific peptide transitions during predefined retention time (RT) windows...
June 25, 2018: Journal of Proteomics
Pey Yee Lee, Siok-Fong Chin, Teck Yew Low, Rahman Jamal
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide. Biomarkers that can facilitate better clinical management of CRC are in high demand to improve patient outcome and to reduce mortality. In this regard, proteomic analysis holds a promising prospect in the hunt of novel biomarkers for CRC and in understanding the mechanisms underlying tumorigenesis. This review aims to provide an overview of the current progress of proteomic research, focusing on discovery and validation of diagnostic biomarkers for CRC...
June 25, 2018: Journal of Proteomics
Yuan Wei, Chun-Lu Fang, Shu-Jing Liu, Wen-Qi Yang, Li-Shen Wei, Xiao-Juan Lei, Fei Hu, Hao-Ying Huang, Wei Li, Wei Chen, Liang-Ming Li, Yue-Sheng Long
Physical exercise has been reported to increase neurotrophin in brain tissues as hippocampus as well as increased neurotrophic level peripherally in blood plasma and might have an effect on/or affect molecular processes of energy metabolism (and homeostasis). In this study, using quantitative proteomic analysis, we obtained a plasma protein profile from the rat with long-term moderate exercise. A total of 752 proteins were identified in the plasma. Among them, 54 proteins were significant up-regulated and 47 proteins were down-regulated in the plasma of exercise group compared with the control group...
June 25, 2018: Journal of Proteomics
Nilubon Singhto, Visith Thongboonkerd
Deposition of calcium oxalate (CaOx) crystals in renal interstitium is one of the key factors that cause progressive inflammation in kidney stone disease. Macrophages are responsible for elimination of these crystals but their roles to worsen inflammatory process remain under-investigated. This study thus aimed to define roles of exosomes released from macrophages exposed to CaOx crystals in mediating subsequent inflammatory cascades. Macrophages were incubated with or without CaOx monohydrate (COM) crystals for 16 h and their exosomes were isolated...
June 25, 2018: Journal of Proteomics
Laura Ceballos-Laita, Elain Gutierrez-Carbonell, Hiroyuki Imai, Anunciación Abadía, Matsuo Uemura, Javier Abadía, Ana Flor López-Millán
The aim of this work was to assess the effects of manganese (Mn) toxicity on the proteome of tomato roots using two proteomic approaches, shotgun and two-dimensional electrophoresis. The shotgun approach yielded 367 reliable proteins, whereas the 2-DE approach detected 340 consistent spots. The 2-DE method found 54 proteins changing in relative abundance in the excess Mn treatment, whereas the shotgun detected changes in 118 proteins. Only 7% of the differential proteins were found by both methods, illustrating their complementary nature...
June 25, 2018: Journal of Proteomics
Reema Banarjee, Akshay Sharma, Shakuntala Bai, Arati Deshmukh, Mahesh Kulkarni
Endothelial dysfunction is one of the primary steps in the development of diabetes associated cardiovascular diseases. Hyperglycemic condition in diabetes promotes accumulation of advanced glycation end products (AGEs) in the plasma, that interact with the receptor for AGEs (RAGE) present on the endothelial cells and negatively affect their function. Using Human umbilical vascular endothelial cells (HUVECs) in culture, the effect of glycated human serum albumin on global proteomic changes was studied by SWATH-MS, a label free quantitative proteomic approach...
June 21, 2018: Journal of Proteomics
Hao Wu, Kaijie Xiao, Zhixin Tian
Core histones and their PTMs play important roles in regulating gene transcription and other DNA-related processes. The study of core histones PTMs, their cross-talk and functional roles is not only of broad biological significance but also of wide pathological and clinical relevance. Having the strength of comprehensive proteoform identification with 100% amino acid sequence coverage and combinatorial PTMs, top-down proteomics has become the state-of-the-art analytical tool for combinatorial PTM characterization of core histones...
June 20, 2018: Journal of Proteomics
Qingfeng Meng, Ravi Gupta, Chul Woo Min, Jongyun Kim, Katharina Kramer, Yiming Wang, Sang-Ryeol Park, Iris Finkemeier, Sun Tae Kim
Previously, we reported a novel Magnaporthe oryzae- secreted protein MSP1, which triggers cell death and pathogen-associated molecular pattern (PAMP)-triggered immune (PTI) responses in rice. To investigate the MSP1 induced defense response in rice at the protein level, we employed a label-free quantitative proteomic approach, in parallel with flg22 treatment, which is a well-known elicitor. Exogenous application of MSP1 to rice leaves induced an oxidative burst, MAPK3/6 activation, and activation of pathogenesis-related genes (DUF26, PBZ, and PR-10)...
June 19, 2018: Journal of Proteomics
Huan Zhang, Liurong Fang, Xinyu Zhu, Dang Wang, Shaobo Xiao
Protein lysine ubiquitination is a dynamic reversible post-translational modification that plays key roles in modulating different cellular processes. Porcine reproductive and respiratory syndrome virus (PRRSV) is a notorious pathogen, causing tremendous economic losses for the global swine industry. The possible involvement of ubiquitination in PRRSV infection is unclear. So anti-ubiquitination-based enrichment and LC-MS were performed to investigate the global ubiquitination events triggered by PRRSV infection in pulmonary alveolar macrophages...
June 18, 2018: Journal of Proteomics
Bénédicte Buffin-Meyer, Julie Klein, Benjamin Breuil, Françoise Muller, Panagiotis Moulos, Marion Groussolles, Ourdia Bouali, Jean-Loup Bascands, Stéphane Decramer, Joost P Schanstra
Most of biomarker panels, extracted from single omics traits, still need improvement since they display a gray zone where prediction is uncertain. Here we verified whether a combination of omics traits, fetal urinary metabolites and peptides analyzed in the same sample, improved prediction of postnatal renal function in fetuses with posterior urethral valves (PUV) compared to individual omics traits. Using CE-MS, we explored the urinary metabolome of 13 PUV fetuses with end stage renal disease (ESRD) and 12 PUV fetuses without postnatal ESRD at 2 years postnatally...
June 18, 2018: Journal of Proteomics
Svetlana V Sidorenko, Rustam H Ziganshin, Oksana G Luneva, Leonid I Deev, Natalya V Alekseeva, Georgy V Maksimov, Ryszard Grygorczyk, Sergei N Orlov
No abstract text is available yet for this article.
June 18, 2018: Journal of Proteomics
Chien-Chun Liu, Chih-Chuan Lin, Yung-Chin Hsiao, Po-Jung Wang, Jau-Song Yu
Deinagkistrodon acutus, Trimeresurus stejnegeri, Protobothrops mucrosquamatus, Daboia russelii siamensis, Bungarus multicinctus and Naja atra are the six medically important venomous snake species in Taiwan. In this study, we characterized and compared their venom protein profiles using proteomic approaches. The major snake venom proteins were identified by GeLC-MS/MS and the total venom proteome was characterized by in-solution digestion coupled with LC-MS/MS. A total of 27-52 proteins, categorized into 23 protein families, were identified in each snake's venom...
June 18, 2018: Journal of Proteomics
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