7,193 results match your criteria Journal of Proteome Research [Journal]


Mass Spectrometric Imaging Reveals Temporal and Spatial Dynamics of Bioactive Lipids in Arteries Undergoing Restenosis.

J Proteome Res 2019 Feb 20. Epub 2019 Feb 20.

Restenosis, or re-narrowing of the arterial lumen, is a common recurrent disease following balloon angioplasty and stenting treatments for cardiovascular disease. A major technical barrier for deciphering restenotic mechanisms is the dynamic, spatial profiling of bioactive lipids in the arterial wall, especially in small animals. Here, applying matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI), we conducted the first lipidomic study of temporal-spatial profiling in a small animal model of angioplasty-induced restenosis. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00941DOI Listing
February 2019

Pre-fractionation extends, but also creates a bias in the detectable HLA class Ι ligandome.

J Proteome Res 2019 Feb 20. Epub 2019 Feb 20.

HLA class Ι molecules can present a range of cellular alterations (mutations, changes in protein copy number, aberrant post-translational modifications or pathogen proteins) to CD8+ T lymphocytes, in the form of HLA peptide ligands. At any given moment, tens of thousands of different self and foreign HLA class Ι peptides may be presented on the cell surface by HLA class Ι complexes. Due to the enormous biochemical diversity and low abundance of each of these peptides, HLA ligandome analysis presents unique challenges. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00821DOI Listing
February 2019

Sequential Windowed Acquisition of Reporter Masses for Quantitation-First Proteomics.

J Proteome Res 2019 Feb 19. Epub 2019 Feb 19.

The standard approach for proteomic data acquisition of isobaric tagged samples by mass spectrometry is Data Dependent Acquisition (DDA). This semi-stochastic, identification-first paradigm generates a wealth of peptide-level data without regard to relative abundance. We introduce a data acquisition concept called Sequential Windowed Acquisition of Reporter Masses (SWARM). Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00884DOI Listing
February 2019

Depletion of high molecular mass proteins for the identification of small proteins and short open reading frame encoded peptides in cellular proteomes.

J Proteome Res 2019 Feb 19. Epub 2019 Feb 19.

The identification of small proteins and peptides (below ca. 100 to 150 amino acids) in complex biological samples is hampered by the dominance of higher molecular weight proteins. On the other hand, the increasing knowledge about alternative or short open reading frames creates a need for methods that allow the existence of the corresponding gene products to be proven in proteomics experiments. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00948DOI Listing
February 2019

Microbiota metabolism promotes synthesis of the human Ah receptor agonist 2,8-dihydroxyquinoline.

J Proteome Res 2019 Feb 19. Epub 2019 Feb 19.

The Aryl hydrocarbon receptor (AHR) is a major regulator of immune function within the gastrointestinal tract. Resident microbiota are capable influencing AHR-dependent signaling pathways via production of an array of bioactive molecules that act as AHR agonists, such as indole or indole-3-aldehyde. Bacteria produce a number of quinoline derivatives, of which some function as quorum-sensing molecules. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00946
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http://dx.doi.org/10.1021/acs.jproteome.8b00946DOI Listing
February 2019
1 Read

Development of a sensitive, scalable method for spatial, cell-type-resolved proteomics of the human brain.

J Proteome Res 2019 Feb 15. Epub 2019 Feb 15.

While nearly comprehensive proteome coverage can be achieved from bulk tissue or cultured cells, the data usually lacks spatial resolution. As a result, tissue based proteomics averages protein abundance across multiple cell types and/or localisations. With proteomics platforms lacking sensitivity and throughput to undertake deep single-cell proteome studies in order to resolve spatial or cell type dependent protein expression gradients within tissue, proteome analysis has been combined with sorting techniques to enrich for certain cell populations. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00981DOI Listing
February 2019

Disease development is accompanied by changes in bacterial protein abundance and functions in a refined model of dextran sulfate sodium (DSS)-induced colitis.

J Proteome Res 2019 Feb 15. Epub 2019 Feb 15.

Using the acute dextran sulfate sodium (DSS)-induced colitis model, studies have demonstrated that intestinal inflammation is accompanied by major changes in the composition of the intestinal microbiota. Only little is known about the microbial changes and more importantly their functional impact in the chronic DSS colitis model. We used a refined model of chronic DSS-induced colitis that reflects typical symptoms of the human disease without detrimental weight loss usually observed in DSS models. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00974
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http://dx.doi.org/10.1021/acs.jproteome.8b00974DOI Listing
February 2019
2 Reads

Localisation of Outer Membrane Proteins in Treponema denticola by Quantitative Proteome Analyses of Outer Membrane Vesicles and Cellular Fractions.

J Proteome Res 2019 Feb 14. Epub 2019 Feb 14.

The identification and localisation of outer membrane proteins (Omps) and lipoproteins in pathogenic treponemes such as T. denticola (periodontitis) and T. pallidum (syphilis) has been challenging. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00860DOI Listing
February 2019

Suspension Trapping (S-Trap) Is Compatible with Typical Protein Extraction Buffers and Detergents for Bottom-Up Proteomics.

J Proteome Res 2019 Feb 20. Epub 2019 Feb 20.

de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine , Weizmann Institute of Science , Rehovot 76100 , Israel.

The analysis of cells and tissue by bottom-up proteomics starts with lysis, followed by in-solution digestion. Lysis buffers commonly used include detergents and other reagents for achieving efficient protein solubility. However, these reagents are, for the most part, incompatible with downstream analytical instrumentation. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00891DOI Listing
February 2019

Preoperative Metabolic Signatures of Prostate Cancer Recurrence Following Radical Prostatectomy.

J Proteome Res 2019 Feb 20. Epub 2019 Feb 20.

School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.

Technological advances in mass spectrometry (MS), liquid chromatography (LC) separations, nuclear magnetic resonance (NMR) spectroscopy, and big data analytics have made possible studying metabolism at an "omics" or systems level. Here, we applied a multiplatform (NMR + LC-MS) metabolomics approach to the study of preoperative metabolic alterations associated with prostate cancer recurrence. Thus far, predicting which patients will recur even after radical prostatectomy has not been possible. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00926DOI Listing
February 2019

An improved method for measuring absolute metabolite concentrations in small biofluid or tissue samples.

J Proteome Res 2019 Feb 13. Epub 2019 Feb 13.

The measurement of absolute metabolite concentrations in small samples remains a significant analytical challenge. This is particularly the case when the sample volume is only a few microlitres or less and cannot be determined accurately via direct measurement. We previously developed volume determination with two standards (VDTS) as a method to address this challenge for biofluids. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00773DOI Listing
February 2019

Metabolomics Reveals Anaerobic Bacterial Fermentation and Hypoxanthine Accumulation for Fibrinous Pleural Effusions in Children with Pneumonia.

J Proteome Res 2019 Feb 19. Epub 2019 Feb 19.

Department of Medical Imaging and Intervention, Imaging Core Laboratory, Institute for Radiological Research, and Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, College of Medicine , Chang Gung University , Taoyuan 333 , Taiwan.

Fibrin formation in infectious parapneumonic effusion (IPE) characterizes complicated parapneumonic effusion and is important for providing guidelines for the management of IPEs that require aggressive interventions. We aim to identify metabolic mechanisms associated with bacterial invasion, inflammatory cytokines, and biochemical markers in cases of fibrinous infectious pleural effusions in children with pneumonia. Pleural fluid metabolites were determined by H nuclear magnetic resonance spectroscopy. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00864DOI Listing
February 2019
1 Read
4.245 Impact Factor

Cytokine Profiles in Autoantibody Defined Subgroups of Systemic Lupus Erythematosus.

J Proteome Res 2019 Feb 18. Epub 2019 Feb 18.

Computational Life Science Cluster (CLiC), Department of Chemistry , Umeå University , 901 87 Umeå , Sweden.

The aim of this study was to evaluate how the cytokine profiles differed between autoantibody based subgroups of systemic lupus erythematosus (SLE). SLE is a systemic autoimmune disease, characterized by periods of flares (active disease) and remission (inactive disease). The disease can affect many organ systems, e. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00811DOI Listing
February 2019
2 Reads

Analyzing Change in Protein Stability Associated with Single Point Deletions in a Newly Defined Protein Structure Database.

J Proteome Res 2019 Feb 18. Epub 2019 Feb 18.

Department of Structural Biology , Weizmann Institute of Science , Rehovot 76100 , Israel.

Protein backbone alternation due to insertion/deletion or mutation operation often results in a change of fundamental biophysical properties of proteins. The proposed work intends to encode the protein stability changes associated with single point deletions (SPDs) of amino acids in proteins. The encoding will help in the primary screening of detrimental backbone modifications before opting for expensive in vitro experimentations. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00048DOI Listing
February 2019

Proteomic Atlas of the Human Brain in Alzheimer's Disease.

J Proteome Res 2019 Feb 20. Epub 2019 Feb 20.

Morgridge Institute for Research , Madison , Wisconsin 53706 , United States.

The brain represents one of the most divergent and critical organs in the human body. Yet, it can be afflicted by a variety of neurodegenerative diseases specifically linked to aging, about which we lack a full biomolecular understanding of onset and progression, such as Alzheimer's disease (AD). Here we provide a proteomic resource comprising nine anatomically distinct sections from three aged individuals, across a spectrum of disease progression, categorized by quantity of neurofibrillary tangles. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00004DOI Listing
February 2019

Multi-omic profiling of TKI resistant K562 cells suggests metabolic reprogramming to promote cell survival.

J Proteome Res 2019 Feb 7. Epub 2019 Feb 7.

Resistance to chemotherapy can occur through a wide variety of mechanisms. Resistance to tyrosine kinase inhibitors (TKIs) often arises from kinase mutations-however, "off-target" resistance occurs but is poorly understood. Previously, we established cell line resistance models for three TKIs used in chronic myeloid leukemia treatment, and found that resistance was not attributed entirely to failure of kinase inhibition. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00028DOI Listing
February 2019
1 Read

Quantitative Proteomics Reveals Changes in Vero Cells in Response to Porcine Epidemic Diarrhea Virus.

J Proteome Res 2019 Feb 18. Epub 2019 Feb 18.

College of Veterinary Medicine , South China Agricultural University , Guangzhou 510642 , China.

Outbreaks of porcine epidemic diarrhea virus (PEDV) have caused significant lethality rates in neonatal piglets, which pose a serious threat to the swine industry worldwide. Available commercial vaccines fail to protect against the emergence of high virulence of PEDV variants. Therefore, the endemic state of the PEDV infection in suckling piglets highlights the urgent need for uncovering the molecular determinants of the disease pathogenesis. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00897DOI Listing
February 2019
4 Reads

Comparison of Protein Quantification in a Complex Background by DIA and TMT Workflows with Fixed Instrument Time.

J Proteome Res 2019 Feb 20. Epub 2019 Feb 20.

Biognosys AG , Wagistrasse 21 , 8952 Schlieren , Switzerland.

Label-free quantification (LFQ) and isobaric labeling quantification (ILQ) are among the most popular protein quantification workflows in discovery proteomics. Here, we compared the TMT SPS/MS3 10-plex workflow to a label free single shot data-independent acquisition (DIA) workflow on a controlled sample set. The sample set consisted of ten samples derived from 10 biological replicates of mouse cerebelli spiked with the UPS2 protein standard in five different concentrations. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00898DOI Listing
February 2019

Detecting modifications in proteomics experiments with Param-Medic.

J Proteome Res 2019 Feb 4. Epub 2019 Feb 4.

Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in re-analysis of public data sets, this experimental metadata may be missing or inaccurate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling and tandem mass tags, as well as enrichment of phosphorylated peptides, directly from a given set of mass spectra. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00954DOI Listing
February 2019
2 Reads

A Novel Truncated Form of Nephronectin Is Present in Small Extracellular Vesicles Isolated from 66cl4 Cells.

J Proteome Res 2019 Feb 13. Epub 2019 Feb 13.

Cancer Clinic , St. Olav's Hospital, Trondheim University Hospital , Trondheim , Norway.

Extracellular vesicles are emerging as biomarkers in breast cancer. Our recent report suggested that an intracellular granular staining pattern of the extracellular matrix protein nephronectin (NPNT) in breast tumor sections correlated with a poor prognosis. Furthermore, the results showed that NPNT is localized in extracellular vesicles derived from mouse breast cancer cells. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00859DOI Listing
February 2019

Metabolomic and Immunological Profiling of Respiratory Syncytial Virus Infection after Intranasal Immunization with a Subunit Vaccine Candidate.

J Proteome Res 2019 Feb 8. Epub 2019 Feb 8.

VIDO-InterVac , University of Saskatchewan , Saskatoon S7N 5E3 , Canada.

Respiratory syncytial virus (RSV) is a significant cause of mortality and morbidity in infants, the elderly, immunocompromised individuals, and patients with congenital heart diseases. Despite extensive efforts, a vaccine against RSV is still not available. We have previously reported the development of a subunit vaccine (ΔF/TriAdj) composed of a truncated version of the fusion protein (ΔF) and a polymer-based combination adjuvant (TriAdj). Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00806DOI Listing
February 2019

Modulation of Lipid Metabolism by Celastrol.

J Proteome Res 2019 Feb 12. Epub 2019 Feb 12.

State Key Laboratory of Phytochemistry and Plant Resources in West China , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , China.

Hyperlipidemia, characterized by high serum lipids, is a risk factor for cardiovascular disease. Recent studies have identified an important role for celastrol, a proteasome inhibitor isolated from Tripterygium wilfordii Hook. F. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00797
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http://dx.doi.org/10.1021/acs.jproteome.8b00797DOI Listing
February 2019
3 Reads

Targeting XIAP and PPARγ in granulosa cell tumors alters metabolic signaling.

J Proteome Res 2019 Feb 1. Epub 2019 Feb 1.

Ovarian granulosa cell tumors (GCT) are hormonally-active cancers characterized by indolent growth and late, invasive relapse. No therapies have yet proven to be efficacious. We previously reported that inhibition of the anti-apoptotic X-linked inhibitor of apoptosis protein (XIAP) removes transrepression of the pro-proliferative nuclear receptor, peroxisome proliferator-activated receptor (PPAR)-γ, in a GCT-derived cell line, KGN. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00917
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http://dx.doi.org/10.1021/acs.jproteome.8b00917DOI Listing
February 2019
3 Reads

Detection of Six Commercially Processed Soy Ingredients in an Incurred Food Matrix Using Parallel Reaction Monitoring.

J Proteome Res 2019 Feb 11. Epub 2019 Feb 11.

Food Allergy Research and Resource Program, Department of Food Science and Technology , University of Nebraska , Lincoln , Nebraska 68588 , United States.

Soybeans are one of the major allergenic foods in many countries. Soybeans are commonly processed into different types of soy ingredients to achieve the desired properties. The processing, however, may affect the protein profiles and protein structure, thus affecting the detection of soy proteins. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00689DOI Listing
February 2019
1 Read

Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.

J Proteome Res 2019 Jan 31. Epub 2019 Jan 31.

Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, co-limitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00761DOI Listing
January 2019

Proteomes of Paired Human Cerebrospinal Fluid and Plasma: Relation to Blood-Brain Barrier Permeability in Older Adults.

J Proteome Res 2019 Feb 15. Epub 2019 Feb 15.

Old Age Psychiatry, Department of Psychiatry , CHUV , 1011 Lausanne , Switzerland.

The systems-level relationship between the proteomes of cerebrospinal fluid (CSF) and plasma has not been comprehensively described so far. Recently developed shotgun proteomic workflows allow for deeper characterization of the proteomes from body fluids in much larger sample size. We deployed state-of-the-art mass spectrometry-based proteomics in paired CSF and plasma samples volunteered by 120 elders with and without cognitive impairment to comprehensively characterize and examine compartmental proteome differences and relationships between both body fluids. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00809DOI Listing
February 2019

Metabolomic Profiling of Aqueous Humor in Glaucoma Points to Taurine and Spermine Deficiency: Findings from the Eye-D Study.

J Proteome Res 2019 Feb 11. Epub 2019 Feb 11.

Unité Mixte de Recherche MITOVASC, équipe Mitolab, Centre National de la Recherche Scientifique 6015, Institut National de la Santé et de la Recherche Médicale U1083 , Université d'Angers , Angers 49035 , France.

We compared the metabolomic profile of aqueous humor from patients with primary open-angle glaucoma (POAG; n = 26) with that of a group of age- and sex-matched non-POAG controls (n = 26), all participants undergoing cataract surgery. Supervised paired partial least-squares discriminant analysis showed good predictive performance for test sets with a median area under the receiver operating characteristic of 0.89 and a p-value of 0. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00915DOI Listing
February 2019

ELM-MHC: An Improved MHC Identification Method with Extreme Learning Machine Algorithm.

J Proteome Res 2019 Feb 18. Epub 2019 Feb 18.

Institute of Fundamental and Frontier Sciences , University of Electronic Science and Technology of China , Chengdu 610054 , China.

The major histocompatibility complex (MHC) is a term for all gene groups of a major histocompatibility antigen. It binds to peptide chains derived from pathogens and displays pathogens on the cell surface to facilitate T-cell recognition and perform a series of immune functions. MHC molecules are critical in transplantation, autoimmunity, infection, and tumor immunotherapy. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00012DOI Listing
February 2019

Proteomic Sample Preparation through Extraction by Unspecific Adsorption on Silica Beads for ArgC-like Digestion.

J Proteome Res 2019 Feb 13. Epub 2019 Feb 13.

Institute of Pharmaceutical Chemistry , Goethe-University , Frankfurt am Main 60438 , Germany.

Sample preparation for mass-spectrometry-based proteomic analyses usually requires intricate, multistep workflows that are often limited in capacity or suffer from sample loss. Here, we introduce a lean adsorption-based protocol (ABP) for the extraction of proteins from fresh cell lysates that enables us to modify and tag protein samples under harsh conditions, such as organic solvents, high salt concentrations, or low pH values. This offers high versatility while also reducing the required steps in the preparation process significantly. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00882DOI Listing
February 2019

Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents.

J Proteome Res 2019 Feb 18. Epub 2019 Feb 18.

Institute of Molecular Pathology (IMP) , Vienna BioCenter (VBC) , Vienna 1030 , Austria.

Cross-linking mass spectrometry is becoming increasingly popular, and current advances are widening the applicability of the technique so that it can be utilized by nonspecialist laboratories. Specifically, the use of novel mass-spectrometry-cleavable (MS-cleavable) reagents dramatically reduces the complexity of the data by providing (i) characteristic reporter ions and (ii) the mass of the individual peptides rather than that of the cross-linked moiety. However, optimum acquisition strategies to obtain the best-quality data for such cross-linkers with higher energy C-trap dissociation (HCD) alone are yet to be achieved. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00947DOI Listing
February 2019

Multi-omic Analyses Reveal Minimal Impact of the CRISPR-Cas9 Nuclease on Cultured Human Cells.

J Proteome Res 2019 Feb 4. Epub 2019 Feb 4.

Interdisciplinary Research Center on Biology and Chemistry , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 26 Qiuyue Road , Pudong , Shanghai 201210 , China.

The CRISPR-Cas9 system is a genomic editing tool widely used in basic research and under investigation for potential applications in gene therapies for human diseases. To accomplish genomic editing, the system requires the expression of a prokaryotic DNA endonuclease enzyme, Cas9, in host cells. Previous studies have mainly focused on the specificity of Cas9 on the host genome, and thus it is unclear whether this bacterium-derived enzyme affects the protein homeostasis of host cells. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00751DOI Listing
February 2019
4.245 Impact Factor

Urine Nuclear Magnetic Resonance (NMR) Metabolomics in Age-Related Macular Degeneration.

J Proteome Res 2019 Feb 6. Epub 2019 Feb 6.

CICECO- Aveiro Institute of Materials (CICECO/UA), Department of Chemistry , University of Aveiro , 3810-193 Aveiro , Portugal.

Biofluid biomarkers of age-related macular degeneration (AMD) are still lacking, and their identification is challenging. Metabolomics is well-suited to address this need, and urine is a valuable accessible biofluid. This study aimed to characterize the urinary metabolomic signatures of patients with different stages of AMD and a control group (>50 years). Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00877
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http://dx.doi.org/10.1021/acs.jproteome.8b00877DOI Listing
February 2019
5 Reads

LasB and CbpD Virulence Factors of Pseudomonas aeruginosa Carry Multiple Post-Translational Modifications on Their Lysine Residues.

J Proteome Res 2019 Jan 31. Epub 2019 Jan 31.

Normandie University, UNIROUEN, INSA Rouen, CNRS, PBS , 76000 Rouen , France.

Pseudomonas aeruginosa is a multi-drug resistant human pathogen largely involved in nosocomial infections. Today, effective antibacterial agents are lacking. Exploring the bacterial physiology at the post-translational modifications (PTM) level may contribute to the renewal of fighting strategies. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00556
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http://dx.doi.org/10.1021/acs.jproteome.8b00556DOI Listing
January 2019
6 Reads

Proteomic Analysis of Azacitidine-Induced Degradation Profiles Identifies Multiple Chromatin and Epigenetic Regulators Including Uhrf1 and Dnmt1 as Sensitive to Azacitidine.

J Proteome Res 2019 Feb 7. Epub 2019 Feb 7.

School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom.

DNA methylation is a critical epigenetic modification that is established and maintained across the genome by DNA methyltransferase enzymes (Dnmts). Altered patterns of DNA methylation are a frequent occurrence in many tumor genomes, and inhibitors of Dnmts have become important epigenetic drugs. Azacitidine is a cytidine analog that is incorporated into DNA and induces the specific inhibition and proteasomal-mediated degradation of Dnmts. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00745DOI Listing
February 2019

Sampling of Tissues with Laser Ablation for Proteomics: Comparison of Picosecond Infrared Laser and Microsecond Infrared Laser.

J Proteome Res 2019 Jan 29. Epub 2019 Jan 29.

Institute of Clinical Chemistry and Laboratory Medicine , University Medical Center Hamburg-Eppendorf , Martinistraße 52 , 20246 Hamburg , Germany.

It was recently shown that sampling of tissues with a picosecond infrared laser (PIRL) for analysis with bottom-up proteomics is advantageous compared to mechanical homogenization. Because the cold ablation of tissues with PIRL irradiation is soft, proteins remain intact and even enzymatic activities are detectable in PIRL homogenates. In contrast, it was observed that irradiation of tissues with a microsecond infrared laser (MIRL) heats the tissue, thereby causing significant damage. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00009DOI Listing
January 2019

Identification and Characterization of Canine Ligament Progenitor Cells and Their Extracellular Matrix Niche.

J Proteome Res 2019 Feb 7. Epub 2019 Feb 7.

Department of Musculoskeletal Biology , Institute of Ageing and Chronic Disease, University of Liverpool , William Henry Duncan Building, 6 West Derby Street , Liverpool , L7 8TX , United Kingdom.

Ligaments are prone to injury and degeneration in humans and animals, however the healing potential of ligament is poor and current treatment options ineffective. Stem cell-based therapies hold potential for treatment of ligament injuries. This study aimed to characterize a ligament progenitor cell (LPC) population and to identify specific niche components which could promote the survival and function of LPCs. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00933DOI Listing
February 2019

P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data.

J Proteome Res 2019 Feb 6. Epub 2019 Feb 6.

Computing & Analytics Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States.

The use of mass-spectrometry-based techniques for global protein profiling of biomedical or environmental experiments has become a major focus in research centered on biomarker discovery; however, one of the most important issues recently highlighted in the new era of omics data generation is the ability to perform analyses in a robust and reproducible manner. This has been hypothesized to be one of the issues hindering the ability of clinical proteomics to successfully identify clinical diagnostic and prognostic biomarkers of disease. P-Mart ( https://pmart. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00840DOI Listing
February 2019

Simulation and Reconstruction of Metabolite-Metabolite Association Networks Using a Metabolic Dynamic Model and Correlation Based Algorithms.

J Proteome Res 2019 Feb 4. Epub 2019 Feb 4.

Laboratory of Systems and Synthetic Biology , Wageningen University & Research , Stippeneng 4 , 6708WE Wageningen , The Netherlands.

Biological networks play a paramount role in our understanding of complex biological phenomena, and metabolite-metabolite association networks are now commonly used in metabolomics applications. In this study we evaluate the performance of several network inference algorithms (PCLRC, MRNET, GENIE3, TIGRESS, and modifications of the MRNET algorithm, together with standard Pearson's and Spearman's correlation) using as a test case data generated using a dynamic metabolic model describing the metabolism of arachidonic acid (consisting of 83 metabolites and 131 reactions) and simulation individual metabolic profiles of 550 subjects. The quality of the reconstructed metabolite-metabolite association networks was assessed against the original metabolic network taking into account different degrees of association among the metabolites and different sample sizes and noise levels. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00781DOI Listing
February 2019

Active Instrument Engagement Combined with a Real-Time Database Search for Improved Performance of Sample Multiplexing Workflows.

J Proteome Res 2019 Feb 4. Epub 2019 Feb 4.

Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

Quantitative proteomics employing isobaric reagents has been established as a powerful tool for biological discovery. Current workflows often utilize a dedicated quantitative spectrum to improve quantitative accuracy and precision. A consequence of this approach is a dramatic reduction in the spectral acquisition rate, which necessitates the use of additional instrument time to achieve comprehensive proteomic depth. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00899
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http://dx.doi.org/10.1021/acs.jproteome.8b00899DOI Listing
February 2019
2 Reads

A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45 810 Computational Analysis Runs.

J Proteome Res 2019 Jan 30. Epub 2019 Jan 30.

ProCan , Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead , NSW 2145 , Australia.

In the current study, we show how ProCan90, a curated data set of HEK293 technical replicates, can be used to optimize the configuration options for algorithms in the OpenSWATH pipeline. Furthermore, we use this case study as a proof of concept for horizontal scaling of such a pipeline to allow 45 810 computational analysis runs of OpenSWATH to be completed within four and a half days on a budget of US $10 000. Through the use of Amazon Web Services (AWS), we have successfully processed each of the ProCan 90 files with 506 combinations of input parameters. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00709DOI Listing
January 2019
1 Read

Integrative Transcriptome and Proteome Analysis Identifies Major Metabolic Pathways Involved in Pepper Fruit Development.

J Proteome Res 2019 Jan 29. Epub 2019 Jan 29.

Longping Branch , Graduate School of Hunan University , Changsha 410125 , China.

Pepper ( Capsicum annuum L.) fruit development is a complex and genetically programmed process. In this study, we conducted integrative analysis of transcriptome and proteome profiles during pepper fruit development. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00673
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http://dx.doi.org/10.1021/acs.jproteome.8b00673DOI Listing
January 2019
3 Reads

Quantifying Competition among Mitochondrial Protein Acylation Events Induced by Ethanol Metabolism.

J Proteome Res 2019 Jan 31. Epub 2019 Jan 31.

Skaggs School of Pharmacy and Pharmaceutical Sciences , University of Colorado Anschutz Medical Campus , Aurora , Colorado 80045 , United States.

Mitochondrial dysfunction is one of many key factors in the etiology of alcoholic liver disease (ALD). Lysine acetylation is known to regulate numerous mitochondrial metabolic pathways, and recent reports demonstrate that alcohol-induced protein acylation negatively impacts these processes. To identify regulatory mechanisms attributed to alcohol-induced protein post-translational modifications, we employed a model of alcohol consumption within the context of wild type (WT), sirtuin 3 knockout (SIRT3 KO), and sirtuin 5 knockout (SIRT5 KO) mice to manipulate hepatic mitochondrial protein acylation. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00800
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http://dx.doi.org/10.1021/acs.jproteome.8b00800DOI Listing
January 2019
4 Reads

pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data.

J Proteome Res 2019 Jan 28. Epub 2019 Jan 28.

National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States.

Prior to statistical analysis of mass spectrometry (MS) data, quality control (QC) of the identified biomolecule peak intensities is imperative for reducing process-based sources of variation and extreme biological outliers. Without this step, statistical results can be biased. Additionally, liquid chromatography-MS proteomics data present inherent challenges due to large amounts of missing data that require special consideration during statistical analysis. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00760DOI Listing
January 2019

A Markov Chain Monte Carlo Method for Estimating the Statistical Significance of Proteoform Identifications by Top-Down Mass Spectrometry.

J Proteome Res 2019 Jan 28. Epub 2019 Jan 28.

Department of BioHealth Informatics , Indiana University-Purdue University Indianapolis , Indianapolis , Indiana 46202 , United States.

Top-down mass spectrometry is capable of identifying whole proteoform sequences with multiple post-translational modifications because it generates tandem mass spectra directly from intact proteoforms. Many software tools, such as ProSightPC, MSPathFinder, and TopMG, have been proposed for identifying proteoforms with modifications. In these tools, various methods are employed to estimate the statistical significance of identifications. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00562DOI Listing
January 2019

Deuterium-Free, Three-Plexed Peptide Diethylation for Highly Accurate Quantitative Proteomics.

J Proteome Res 2019 Jan 29. Epub 2019 Jan 29.

Center for RNA Research , Institute for Basic Science (IBS) , Seoul 08826 , Korea.

The deuterium, a frequently used stable isotope in isotopic labeling for quantitative proteomics, could deteriorate the accuracy and precision of proteome quantification owing to the retention time shift of deuterated peptides from the hydrogenated counterpart. We introduce a novel three-plexed peptide "diethylation" using only C isotopologues of acetaldehyde and demonstrate that the accuracy and precision of our method in proteome quantification are significantly superior to the conventional deuterium-based dimethylation labeling in both a single-shot and multidimensional LC-MS/MS analysis of the HeLa proteome. Furthermore, in time-resolved profiling of Xenopus laevis early embryogenesis, our 3-plexed diethylation outperformed isobaric labeling approaches in terms of the quantification accuracy or the number of protein identifications, generating more than two times more differentially expressed proteins. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00775DOI Listing
January 2019
4.245 Impact Factor

Peptidomics analysis of milk protein-derived peptides released over time in the preterm infant stomach.

J Proteome Res 2019 Jan 14. Epub 2019 Jan 14.

Over the course of milk digestion, native milk proteases and infant digestive proteases fragment intact proteins into peptides with potential bioactivity. This study investigated the release of peptides over three hours of gastric digestion in 14 preterm infant sample sets. The peptide content was extracted and analyzed from milk and gastric samples via Orbitrap tandem mass spectrometry. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00604DOI Listing
January 2019

MPK4 Phosphorylation Dynamics and Interacting Proteins in Plant Immunity.

J Proteome Res 2019 Jan 28. Epub 2019 Jan 28.

Thermo Fisher Scientific , 1400 Northpoint Parkway , West Palm Beach , Florida 33407 , United States.

Arabidopsis MAP kinase 4 (MPK4) has been proposed to be a negative player in plant immunity, and it is also activated by pathogen-associated molecular patterns (PAMPs), such as flg22. The molecular mechanisms by which MPK4 is activated and regulates plant defense remain elusive. In this study, we investigated Arabidopsis defense against a bacterial pathogen Pseudomonas syringae pv tomato ( Pst) DC3000 when Brassica napus MPK4 ( BnMPK4) is overexpressed. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00345
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http://dx.doi.org/10.1021/acs.jproteome.8b00345DOI Listing
January 2019
6 Reads

Proteomics analysis reveals that structural proteins of the virion core and involved in gene expression are the main source for HLA class II ligands in vaccinia virus-infected cells.

J Proteome Res 2019 Jan 10. Epub 2019 Jan 10.

Protective cellular and humoral immune responses require previous recognition of viral antigenic peptides complexed with HLA class II molecules on the surface of the antigen presenting cells. The HLA class II-restricted immune response is important for the control and the clearance of poxvirus infection including vaccinia virus (VACV), the vaccine used in the worldwide eradication of smallpox. In this study, a mass spectrometry analysis was used to identify VACV ligands bound to HLA-DR and -DP class II molecules present on the surface of VACV-infected cells. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00595
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http://dx.doi.org/10.1021/acs.jproteome.8b00595DOI Listing
January 2019
7 Reads
4.245 Impact Factor

Serum Metabolomics Reveals That Gut Microbiome Perturbation Mediates Metabolic Disruption Induced by Arsenic Exposure in Mice.

J Proteome Res 2019 Jan 25. Epub 2019 Jan 25.

Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.

Arsenic contamination in drinking water has been a worldwide health concern for decades. In addition to being a well-recognized carcinogen, arsenic exposure has also been linked to diabetes, neurological effects, and cardiovascular diseases. Recently, increasing evidence has indicated that gut microbiome is an important risk factor in modulating the development of diseases. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00697
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http://dx.doi.org/10.1021/acs.jproteome.8b00697DOI Listing
January 2019
1 Read
4.245 Impact Factor