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Journal of Proteomics

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https://www.readbyqxmd.com/read/29777872/inventory-of-proteoforms-as-a-current-challenge-of-proteomics-some-technical-aspects
#1
Stanislav Naryzhny
The main intricacy in the human proteome is that it is tremendously complex and composed from diverse and heterogeneous gene products. These products are called protein species or proteoforms and are the smallest units of the proteome. In pursuit of the comprehensive profiling of the human proteome, significant advances in the technology of so called "Top-Down" mass spectrometry based proteomics, have been made. However, the scale of performance of this approach is still far behind the "Bottom-Up", peptide-centric techniques...
May 16, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29777871/pain-therapeutics-from-cone-snail-venoms-from-ziconotide-to-novel-non-opioid-pathways
#2
Helena Safavi-Hemami, Shane E Brogan, Baldomero M Olivera
There have been numerous attempts to develop non-opioid drugs for severe pain, but the vast majority of these efforts have failed. A notable exception is Ziconotide (Prialt®), approved by the FDA in 2004. In this review, we summarize the present status of Ziconotide as a therapeutic drug and introduce a wider framework: the potential of venom peptides from cone snails as a resource providing a continuous pipeline for the discovery of non-opioid pain therapeutics. An auxiliary theme that we hope to develop is that these venoms, already a validated starting point for non-opioid drug leads, should also provide an opportunity for identifying novel molecular targets for future pain drugs...
May 16, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29777870/profiling-modifications-for-glioblastoma-proteome-using-ultra-tolerant-database-search-are-the-peptide-mass-shifts-biologically-relevant-or-chemically-induced
#3
Irina A Tarasova, Peter M Chumakov, Sergei A Moshkovskii, Mikhail V Gorshkov
Peptide mass shifts were profiled using ultra-tolerant database search strategy for shotgun proteomics data sets of human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The main objective of this profiling was revealing the cell response to IFN treatment at the level of protein modifications. To achieve this objective, statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples were analyzed. Detailed analysis of MS/MS spectra allowed further interpretation of the observed mass shifts and differentiation between post-translational and artifact modifications...
May 16, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29758290/proteome-response-of-dental-pulp-cells-to-exogenous-fgf8
#4
Rozaliya Tsikandelova, Petko Mladenov, Sébastien Planchon, Silvia Kalenderova, Maria Dragneva, Zornitsa Mihaylova, Pavel Stanimirov, Vanyo Mitev, Jenny Renaut, Nikolay Ishkitiev
FGF8 specifies early tooth development by directing the migration of the early tooth founder cells to the site of tooth emergence. To date the effect of the FGF8 in adult dental pulp has not been studied. We have assessed the regenerative potential of FGF8 by evaluating changes in the proteome landscape of dental pulp following short- and long-term exposure to recombinant FGF8 protein. In addition, we carried out qRT PCR analysis to determine extracellular/adhesion gene marker expression and assessed cell proliferation and mineralization in response to FGF8 treatment...
May 11, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29753025/identification-and-efficacy-of-glycine-serine-and-threonine-metabolism-in-potentiating-kanamycin-mediated-killing-of-edwardsiella-piscicida
#5
Jin-Zhou Ye, Xiang-Min Lin, Zhi-Xue Cheng, Yu-Bin Su, Wan-Xin Li, Far-Man Ali, Jun Zheng, Bo Peng
We previously showed that glucose potentiated kanamycin to kill multidrug-resistant Edwardsiella piscicida through activation of the TCA cycle. However, whether other regulatory mechanism is involved requires further investigation. By quantitative proteomics technology, iTRAQ, we systematically mapped the altered proteins in the presence of glucose and identified 94 differentially expressed proteins. The analysis of the altered proteins by pathways, amino acid biosynthesis and metabolism were enriched. And the most significantly altered eight amino acids tyrosine, phenylalanine, valine, leucine, isoleucine, glycine, serine and threonine were investigated for their potentiation of kanamycin to kill EIB202, where glycine, serine and threonine showed the strongest efficacy than the others...
May 9, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29751106/curcumin-exerts-its-antitumor-effects-in-a-context-dependent-fashion
#6
Dominique Kreutz, Chomdao Sinthuvanich, Andrea Bileck, Lukas Janker, Besnik Muqaku, Astrid Slany, Christopher Gerner
Proteome profiling profoundly contributes to the understanding of cell response mechanisms to drug actions. Such knowledge may become a key to improve personalized medicine. In the present study, the effects of the natural remedy curcumin on breast cancer model systems were investigated. MCF-7, ZR-75-1 and TGF-β1 pretreated fibroblasts, mimicking cancer-associated fibroblasts (CAFs), were treated independently as well as in tumor cell/CAF co-cultures. Remarkably, co-culturing with CAF-like cells (CLCs) induced different proteome alterations in MCF-7 and ZR-75-1 cells, respectively...
May 8, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29751105/use-of-liquid-isoelectric-focusing-offgel-on-the-discovery-of-meat-tenderness-biomarkers
#7
Lorea R Beldarrain, Noelia Aldai, Brigitte Picard, Enrique Sentandreu, Jose L Navarro, Miguel A Sentandreu
Protein biomarkers of meat tenderness are known to be of primary importance for the prediction of meat quality, and hence, industry profitability. Proteome analysis was performed on meat from 8 Main Anjou beef cattle, previously classified as tender or tough meats by Warner Bratzler shear force measurements. Myofibrillar fraction of Longissimus thoracis muscle was separated by a novel fractionation approach based on liquid isoelectric focusing (OFFGEL) and further analyzed by SDS-PAGE and liquid chromatography coupled to tandem mass spectrometry...
May 8, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29729992/proteomics-functional-characterization-and-antivenom-neutralization-of-the-venom-of-pakistani-russell-s-viper-daboia-russelii-from-the-wild
#8
Tasnim Faisal, Kae Yi Tan, Si Mui Sim, Naeem Quraishi, Nget Hong Tan, Choo Hock Tan
The venom proteome of wild Pakistani Russell's viper (Daboia russelii) was investigated through nano-ESI-LCMS/MS of the reverse-phase HPLC fractions. A total of 54 venom proteins were identified and clustered into 11 protein families. Phospholipase A2 (PLA2 , 63.8%) and Kunitz-type serine protease inhibitor (KSPI, 16.0%) were most abundant, followed by snake venom serine protease (SVSP, 5.5%, mainly Factor V activating enzyme), vascular endothelial growth factor (VEGF, 4.3%), snake venom metalloprotease (SVMP, 2...
May 3, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29729991/subcellular-proteome-profiles-of-different-latex-fractions-revealed-washed-solutions-from-rubber-particles-contain-crucial-enzymes-for-natural-rubber-biosynthesis
#9
Dan Wang, Yong Sun, Lili Chang, Zheng Tong, Quanliang Xie, Xiang Jin, Liping Zhu, Peng He, Hongbin Li, Xuchu Wang
Rubber particle (RP) is a specific organelle for natural rubber biosynthesis (NRB) and storage in rubber tree Hevea brasiliensis. NRB is processed by RP membrane-localized proteins, which were traditionally purified by repeated washing. However, we noticed many proteins in the discarded washing solutions (WS) from RP. Here, we compared the proteome profiles of WS, C-serum (CS) and RP by 2-DE, and identified 233 abundant proteins from WS by mass spectrometry. Many spots on 2-DE gels were identified as different protein species...
May 3, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29729990/quantitative-proteomics-analysis-of-differentially-expressed-proteins-in-ruptured-and-unruptured-cerebral-aneurysms-by-itraq
#10
Pengjun Jiang, Jun Wu, Xin Chen, Bo Ning, Qingyuan Liu, Zhengsong Li, Maogui Li, Fan Yang, Yong Cao, Rong Wang, Shuo Wang
The underlying pathophysiological mechanisms involved in cerebral aneurysms rupture remain unclear. This study was performed to investigate the differentially expressed proteins between ruptured and unruptured aneurysms using quantitative proteomics. The aneurysmal walls of six ruptured aneurysms and six unruptured aneurysms were collected during the surgical operation. The isobaric tags for relative and absolute quantification (iTRAQ) were used to identify the differentially expressed proteins and western blotting was performed to validate the expression of the proteins of interest...
May 3, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29729432/quantitative-proteomics-and-biochemical-analyses-reveal-the-role-of-endoplasmin-in-the-regulation-of-the-expression-and-secretion-of-a-disintegrin-and-metalloproteinase-12
#11
Lipeng Xiong, Wenwen Yan, Emmanuel Zubia, Yanqing Zhou, Yang Zhang, Qianqian Duan, Mahesh Narayan, Guoqiang Xu
A Disintegrin And Metalloproteinase 12 (ADAM12) is highly expressed in multiple cancers such as breast and cervical cancers and its high expression reduces the overall patient survival rate. ADAM12 has two major splicing variants, the long membrane-anchored form ADAM12L and the short secreted form ADAM12S. However, how they are regulated and whether they are modulated similarly or differently in cells are not clear. Here, we use affinity purification and mass spectrometry to identify the ADAM12S-interacting proteins...
May 2, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29709615/common-proteomic-profiles-of-induced-pluripotent-stem-cell-derived-three-dimensional-neurons-and-brain-tissue-from-alzheimer-patients
#12
Mei Chen, Han-Kyu Lee, Lauren Moo, Eugene Hanlon, Thor Stein, Weiming Xia
We established a unique platform for proteomic analysis of cultured three-dimensional (3D) neurons and brain tissue from Alzheimer's disease (AD) patients. We collected peripheral blood mononuclear cells (PBMC), converted PBMC to induced pluripotent stem cell (iPSC) lines, and differentiated the iPSC into human 3D neuro-spheroids. The postmortem brain tissue from the superior frontal cortex, inferior frontal cortex and cerebellum area of the AD patients was compared to the same regions from the control subjects...
April 27, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29704570/proteomic-analysis-of-the-effect-of-plant-derived-smoke-on-soybean-during-recovery-from-flooding-stress
#13
Xinyue Li, Shafiq Ur Rehman, Hisateru Yamaguchi, Keisuke Hitachi, Kunihiro Tsuchida, Takuya Yamaguchi, Yukari Sunohara, Hiroshi Matsumoto, Setsuko Komatsu
Flooding negatively affects the growth of soybean, whereas the plant-derived smoke enhances seedling growth of crops. To clarify the mechanism underlying the recovery from flooding stress, proteomic analysis was performed based on morphological results. Growth of soybean seedlings was inhibited under flooding stress, but it recovered after water removal following treatment with plant-derived smoke. Sucrose/starch metabolism and glycolysis were suppressed in smoke-treated flooded soybean compared to flooded soybean...
April 25, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29704569/protein-biomarkers-associated-with-pain-mechanisms-in-osteoarthritis
#14
Christian S Thudium, Henrik Löfvall, Morten A Karsdal, Anne-Christine Bay-Jensen, Asger Reinstrup Bihlet
Osteoarthritis (OA) is the most common arthritic disease in the world, leading to debilitating pain and destruction of joint tissues. While pain is the hallmark symptom of osteoarthritis, clear associations between pain and disease processes involved in joint deterioration are lacking. OA pain is multifactorial and may arise from multiple distinct or concurrent mechanisms, and may thus present as different pain sub-types. Several biomarkers developed to reflect important pathological processes are available, and associations between such biomarkers and OA pain may give hints to important pathological features, which have not been possible to assess using clinical, radiographic or magnetic resonance imaging techniques...
April 25, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29698803/fasting-and-refeeding-induces-changes-in-the-mouse-hepatic-lipid-droplet-proteome
#15
David A Kramer, Ariel D Quiroga, Jihong Lian, Richard P Fahlman, Richard Lehner
During fasting, the liver increases lipid storage as a mean to reserve and provide energy for vital cellular functions. After re-feeding, hepatocytes rapidly decrease the amount of triacylglycerol that is stored in lipid droplets (LDs), visible as the size of hepatic LDs significantly decreases after re-feeding. Little is known about the changes in the liver LD proteome that occur during the fasting/re-feeding transition. This study aimed to investigate the hepatic LD proteome in fasted and re-fed conditions in the mouse...
April 23, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29698802/histology-guided-proteomic-analysis-to-investigate-the-molecular-profiles-of-clear-cell-renal-cell-carcinoma-grades
#16
Martina Stella, Clizia Chinello, Anna Cazzaniga, Andrew Smith, Manuel Galli, Isabella Piga, Angelica Grasso, Marco Grasso, Marina Del Puppo, Marta Varallo, Giorgio Bovo, Fulvio Magni
Renal Cell Carcinoma (RCC) is the most frequent form of kidney cancer and approximately 80% of cases are defined as clear cell RCC (ccRCC). Among the histopathological factors, tumour grade represents one of the most important parameters to evaluate ccRCC progression. Nonetheless, the molecular processes associated with the grading classification haven't been deeply investigated thus far. Therefore, the aim of this study was to uncover protein alterations associated with different ccRCC grade lesions. Formalin-fixed paraffin-embedded samples from ccRCC patients were analysed by histology-guided MALDI-MSI and shotgun proteomics in order to study the biological processes implicated in ccRCC...
April 23, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29698801/characterization-of-igg-n-glycome-profile-in-colorectal-cancer-progression-by-maldi-tof-ms
#17
Si Liu, Liming Cheng, Yang Fu, Bi-Feng Liu, Xin Liu
Colorectal cancer (CRC) has become one of the most common cancers worldwide and the fifth most prevalent cancer in China with an upward trend in incidence rates. Altered glycosylation significantly affects the structural and functional changes in immunoglobulin G (IgG) and was consequently associated with disease progression. In this study, we explored the association of glycosylation with CRC prognosis through characterizing serum IgG N-glycans derived from individuals consisting of normal, benign colorectal and CRC cohorts in discovery set...
April 23, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29698800/mhc-class-i-presented-antigens-from-malignancies-a-perspective-on-analytical-characterization-immunogenicity
#18
Maike Schmidt, Jennie R Lill
The field of cancer immunotherapy has expanded rapidly in the past few years, with many new approaches entering the clinic for T cell mediated killing of tumors. Several of these clinical approaches involve the exploitation of a CD8 + T cell response against MHC I presented tumor antigens. Here, we describe the types of tumor antigens which are considered as targets in the design of T cell based therapeutic approaches, the rationale for targeting MHC I antigens and the analytical tools commonly employed for the discovery of MHC I presented peptides...
April 23, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29689304/proteomics-of-liquid-biopsies-depicting-rcc-infiltration-into-the-renal-vein-by-ms-analysis-of-urine-and-plasma
#19
Clizia Chinello, Martina Stella, Isabella Piga, Andrew James Smith, Giorgio Bovo, Marta Varallo, Mariia Ivanova, Vanna Denti, Marco Grasso, Angelica Grasso, Marina Del Puppo, Apostolos Zaravinos, Fulvio Magni
Liquid biopsies, as blood and urine, could offer an invaluable, easily accessible source of biomarkers, and evidences for elucidating the pathological processes. Only few studies integrated the proteomes driven by more than one biofluid. Furthermore, it is not clear which biofluid better mirrors the alterations triggered by disease. Venous infiltrating RCC(Renal Cell Carcinoma) could represent an advantageous model for exploring this aspect. Herein, we investigate how blood and urine "proteomically" reflect the changes occurring during RCC infiltration into renal vein(RV) by label-free nLC-ESI-MS/MS...
April 21, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29684686/a-comprehensive-profile-and-inter-individual-variations-analysis-of-the-human-normal-amniotic-fluid-proteome
#20
Xiang Liu, Yijun Song, Zhengguang Guo, Wei Sun, Juntao Liu
Amniotic fluid contains large amounts of proteins produced by amnion epithelial cells, fetal tissues, fetal excretions and placental tissues; thus, it is an important potential source of biomarkers for identifying fetal pathologies. In this study, a pooled AF sample from 7 healthy volunteers was used to provide a comprehensive profile of normal human AF proteome using immunoaffinity depletion of 14 high-abundance proteins. Each individual AF sample was used to analyze inter-individual variations with iTRAQ method...
April 20, 2018: Journal of Proteomics
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