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Journal of Proteome Research

Yipeng Du, Zichao Zhai, Ying Li, Ming Lu, Tanxi Cai, Bo Zhou, Lei Huang, Taotao Wei, Tingting Li
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomic methods have been widely used to identify lysine acylation proteins. However, these experimental approaches often fail to detect proteins in low abundance or absent in specific biological samples. To circumvent these problems, we developed a computational method to predict lysine acylation, including acetylation, malonylation, succinylation, and glutarylation. The prediction algorithm integrated flanking primary sequence determinants and evolutionary conservation of acylated lysine, as well as multiple protein functional annotation features including gene ontology, conserved domains and protein-protein interactions...
October 24, 2016: Journal of Proteome Research
Ingrid Broodman, Jan Lindemans, Jenny van Sten, Rainer Bischoff, Theo M Luider
Lung cancer has the highest mortality rate among cancer patients in the world, in particular because most patients are only diagnosed at an advanced and non-curable stage. Computed tomography (CT) screening on high-risk individuals has shown that early detection could reduce the mortality rate. However, the still high false-positive rate of CT screening may harm healthy individuals because of unnecessary follow-up scans and invasive follow-up procedures. Alternatively, false-negative and indeterminate results may harm patients due to the delayed diagnosis and treatment of lung cancer...
October 21, 2016: Journal of Proteome Research
Carly B Garrison, Kristin J Lastwika, Yuzheng Zhang, Christopher I Li, Paul D Lampe
Proteomic studies can offer information on hundreds to thousands of proteins and potentially provide researchers with a comprehensive understanding of signaling response during stress and disease. Large datasets, such as those obtained in high-dimensional proteomic studies, can be leveraged for pathway analysis to discover or describe the biological implications of clinical disease states. Obesity is a worldwide epidemic that is considered a risk factor for numerous other diseases. We performed analysis on plasma proteomic data from 3 separate sample sets of post-menopausal women to identify the pathways that are altered in subjects with a high body mass index (BMI) compared to normal BMI...
October 21, 2016: Journal of Proteome Research
Tadamoto Isogai, Rob van der Kammen, Onno B Bleijerveld, Soenita S Goerdayal, Elisabetta Argenzio, A F Maarten Altelaar, Metello Innocenti
Formin mDia2 is a cytoskeleton-regulatory protein that switches reversibly between a closed, auto-inhibited and an open, active conformation. Although the open conformation of mDia2 induces actin assembly thereby controlling many cellular processes, mDia2 possesses also actin-independent and conformation-insensitive scaffolding roles related to microtubules and p53, respectively. Thus, we hypothesise that mDia2 may have other unappreciated functions and regulatory modes. Here we identify and validate proteasome and Ubiquitin as mDia2-interacting partners using SILAC-based quantitative proteomics and biochemistry, respectively...
October 21, 2016: Journal of Proteome Research
Uri Keich, William Stafford Noble
No abstract text is available yet for this article.
October 21, 2016: Journal of Proteome Research
Uri Keich, Attila Kertesz-Farkas, William Stafford Noble
No abstract text is available yet for this article.
October 21, 2016: Journal of Proteome Research
Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung
In the post-genomic era, the number of unreviewed protein sequences is remarkably larger and grows tremendously faster than that of reviewed ones. However, existing methods for protein subchloroplast localization often ignore the information from these unlabelled proteins. This paper proposes a multi-label predictor based on ensemble linear neighborhood propagation (LNP), namely LNP-Chlo, which leverages hybrid sequence-based feature information from both labelled and unlabelled proteins for predicting localization of both single- and multi-label chloroplast proteins...
October 21, 2016: Journal of Proteome Research
Brent M Kuenzi, Adam L Borne, Jiannong Li, Eric B Haura, Steven A Eschrich, John M Koomen, Uwe Rix, Paul A Stewart
With continuously increasing scale and depth of coverage in affinity proteomics (AP-MS) data, the analysis and visualization is becoming more challenging. A number of tools have been developed to identify high-confidence interactions; however, a cohesive and intuitive pipeline for analysis and visualization is still needed. Here we present Automated Processing of SAINT Templated Layouts (APOSTL), a freely available Galaxy-integrated software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data...
October 21, 2016: Journal of Proteome Research
Kuo-Hsun Chiu, Ling-Hui Wang, Tsung-Ting Tsai, Huan-Yao Lei, Pao-Chi Liao
The secreted proteins of bacteria are usually accompanied by virulence factors, which can cause inflammation and damage host cells. Identifying the secretomes arising from the interactions of bacteria and host cells could, therefore, increase understanding of the mechanisms during initial pathogenesis. The present study used a host-pathogen coculture system of Helicobacter pylori and monocytes (THP-1 cells) to investigate the secreted proteins associated with initial H. pylori pathogenesis. The secreted proteins from the conditioned media from H...
October 20, 2016: Journal of Proteome Research
Erik Richter, Manuela Harms, Katharina Ventz, Rolf Nölker, Martin J Fraunholz, Jörg Mostertz, Falko Hochgräfe
Internalization of Staphylococcus aureus by non-professional phagocytic cells is a major suspected cause of persistent and difficult-to-treat infections, including pneumonia. In this study, we established an infection model with 16HBE14o- human bronchial epithelial cells and demonstrated internalization, escape from phagosomal clearance and intracellular replication of S. aureus HG001 within the first four hours post-infection. We used quantitative phosphoproteomics to identify characteristic signaling networks in the host at different infection stages...
October 20, 2016: Journal of Proteome Research
Stacy L DeBlasio, Richard S Johnson, Michael J MacCoss, Stewart M Gray, Michelle Cilia
Phloem localization of plant viruses is advantageous for acquisition by sap-sucking vectors but hampers host-virus protein interaction studies. In this study, Potato leafroll virus (PLRV)-host protein complexes were isolated from systemically infected potato, a natural host of the virus. Comparing two different co-immunoprecipitation support matrices coupled to mass spectrometry, we identified 44 potato proteins and one viral protein (P1) specifically associated with virus isolated from infected phloem. An additional 142 proteins interact in complex with virus at varying degrees of confidence...
October 20, 2016: Journal of Proteome Research
Rodolfo Ciuffa, Etienne Caron, Alexander Leitner, Federico Uliana, Matthias Gstaiger, Ruedi Aebersold
NF-κB is a family of ubiquitous dimeric transcription factors that play a role in a myriad of cellular processes, ranging from differentiation to stress response and immunity. In inflammation, activation of NF-κB is mediated by pro-inflammatory cytokines, in particular the prototypic cytokines IL-1β and TNF-α, which trigger the activation of complex signaling cascades. In spite of decades of research, the system level understanding of TNF-α signaling is still incomplete. This is partially due to the limited knowledge at the proteome level...
October 20, 2016: Journal of Proteome Research
Ju Yeon Lee, Hyun Kyoung Lee, Gun Wook Park, Heeyoun Hwang, Hoi Keun Jeong, Ki Na Yun, Eun Sun Ji, Kwang Hoe Kim, Jun Seok Kim, Jong Won Kim, Sung Ho Yun, Chi-Won Choi, Seung Il Kim, Jong-Sun Lim, Seul-Ki Jeong, Young-Ki Paik, Soo-Youn Lee, Jisook Park, Su Yeon Kim, Young-Jin Choi, Yong-In Kim, Jawon Seo, Je-Yoel Cho, Myoung Jin Oh, Nari Seo, Hyun Joo An, Jin Young Kim, Jong Shin Yoo
Glycoprotein conformations are complex and heterogeneous. Currently, site-specific characterization of glycopeptides is a challenge. Herein, we sought to establish an efficient method of N-glycoprotein characterization using mass spectrometry. Using alpha-1-acid glycoprotein (AGP) as a model N-glycoprotein, its tryptic N-glycopeptides were identified, and the reproducibility of the data was examined in seven laboratories running different liquid chromatography-mass tandem spectrometry (LC-MS/MS) platforms. We used three test samples and one blind sample to evaluate instrument performance with entire sample preparation workflow...
October 19, 2016: Journal of Proteome Research
Nathan J Hare, Ling Y Lee, Ian Loke, Warwick J Britton, Bernadette M Saunders, Morten Thaysen-Andersen
Tuberculosis (TB) remains a prevalent and lethal infectious disease. The glycobiology associated with Mycobacterium tuberculosis infection of front-line alveolar macrophages is still unresolved. Herein, we investigated the regulation of protein N-glycosylation in human macrophages and their secreted microparticles (MPs) used for intercellular communication upon M. tb infection. LC-MS/MS-based proteomics and glycomics were performed to monitor the regulation of glycosylation enzymes and receptors and the N-glycome in in vitro-differentiated macrophages and in isolated MPs upon M...
October 19, 2016: Journal of Proteome Research
Mie Rostved Rasmussen, Kirstine Lykke Nielsen, Mia Roest Laursen, Camilla Bak Nielsen, Pia Svendsen, Henrik Dimke, Erik Ilsø Christensen, Mogens Johannsen, Søren Kragh Moestrup
Loss-of-function mutations in the transmembrane ABCC6 transport protein cause pseudoxanthoma elasticum - an ectopic, metabolic mineralization disorder affecting the skin, eye and vessels. ABCC6 is assumed to mediate efflux of one or several small molecule compounds from the liver cytosol to the circulation. Untargeted metabolomics using liquid chromatography mass spectrometry was employed to inspect liver cytosolic extracts from mice with targeted disruption of the Abcc6 gene. Absence of the ABCC6 protein induced an altered profile of metabolites in the liver causing accumulation of compounds as more features were upregulated than downregulated in ABCC6-deficient mice...
October 19, 2016: Journal of Proteome Research
Matthias Holzlechner, Katharina Strasser, Elitsa Zareva, Luise Steinhaeuser, Hanna Birnleitner, Andrea Beer, Michael Bergmann, Rudolf Oehler, Martina Marchetti-Deschmann
Tissue-resident immune cells differ from the corresponding blood cells in many functional aspects. Although the proteome of blood immune cells is well investigated there are almost no data on tissue-resident immune cells. Here we explored the potential of MALDI-TOF-MS imaging (MSI) to investigate these cells in colon tissue, which exhibits a strong immune infiltration. MSI identified several proteinaceous markers that colocalized with specific structures of the colon such as mucosa or muscularis mucosae in six patients...
October 18, 2016: Journal of Proteome Research
Fengchao Yu, Ning Li, Weichuan Yu
In computational proteomics, identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost associated with database search increases exponentially with respect to the number of modified amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible PTM patterns. To address this issue, one group of methods named restricted tools (including Mascot, Comet, and MS-GF+) only allow a small number of PTM types in database search process...
October 17, 2016: Journal of Proteome Research
Nori Sato, Takako Taniguchi, Yuichiro Goda, Hirofumi Kosaka, Kosaku Higashino, Toshinori Sakai, Shinsuke Katoh, Natsuo Yasui, Koichi Sairyo, Hisaaki Taniguchi
Connective tissues such as tendon, ligament and cartilage are mostly composed of extracellular matrix (ECM). These tissues are insoluble, mainly due to the highly cross-linked ECM proteins such as collagens. Difficulties obtaining suitable samples for mass spectrometric analysis render the application of modern proteomic technologies difficult. Complete solubilization of them would not only elucidate protein composition of normal tissues but also reveal pathophysiology of pathological tissues. Here we report complete solubilization of human Achilles tendon and yellow ligament, which is achieved by chemical digestion combined with successive protease treatment including elastase...
October 17, 2016: Journal of Proteome Research
Jose Antonio Reales-Calderón, Catarina Vaz, Lucía Monteoliva, Gloria Molero, Concha Gil
The effectiveness of macrophages in the response to systemic candidiasis is crucial to an effective clearance of the pathogen. The secretion of proteins, mRNAs, non-coding RNAs and lipids through extracellular vesicles (EVs) is one of the mechanisms of communication between immune cells. EVs change their cargo to mediate different responses, and may play a role in the response against infections. Thus, we have undertaken the first quantitative proteomic analysis on the protein composition of THP1 macrophages-derived EVs during the interaction with Candida albicans...
October 14, 2016: Journal of Proteome Research
Albert Lee, Devin Miller, Roger Henry, Venkata D P Paruchuri, Robert N O'Meally, Tatiana Boronina, Robert N Cole, Natasha E Zachara
O-Linked N-acetyl-β-d-glucosamine (O-GlcNAc) is a dynamic post-translational modification that modifies and regulates over 3000 nuclear, cytoplasmic, and mitochondrial proteins. Upon exposure to stress and injury, cells and tissues increase the O-GlcNAc modification, or O-GlcNAcylation, of numerous proteins promoting the cellular stress response and thus survival. The aim of this study was to identify proteins that are differentially O-GlcNAcylated upon acute oxidative stress (H2O2) to provide insight into the mechanisms by which O-GlcNAc promotes survival...
October 14, 2016: Journal of Proteome Research
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