7,261 results match your criteria Journal of Proteome Research [Journal]


Metabolomics Assay identified a novel virulence-associated siderophore encoded by the High-Pathogenicity Island in uropathogenic Escherichia coli.

J Proteome Res 2019 Apr 17. Epub 2019 Apr 17.

To date, yersiniabactin remains the only identified siderophore encoded by the high pathogenicity island (HPI) in uropathogenic Escherichia coli (UPEC). In the present study, we aim to discover and identify new siderophores in the HPI-dependent biosynthetic pathway using a combinational strategy of metabolomics and genetics. A global metabolome assay of wild-type UTI89, UTI89ΔybtS and UTI89ΔybtS with the substrate addition of salicylic acid found numerous unknown metabolite features that were encoded by the HPI with an obvious substrate dependency on salicylic acid. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00190DOI Listing

Quantitative Interrogation of the Human Kinome Perturbed by Two BRAF Inhibitors.

J Proteome Res 2019 Apr 17. Epub 2019 Apr 17.

Oncogenic BRAF mutations contribute to the development of a number of cancers, and small-molecule BRAF inhibitors have been approved by the Food and Drug Administration (FDA) for anti-cancer therapy. In this study, we employed two targeted quantitative proteomics approaches for monitoring separately the alterations in protein expression and ATP binding affinities of kinases in cultured human melanoma cells elicited by two FDA-approved small-molecule BRAF inhibitors, dabrafenib and vemurafenib. Our results showed that treatment with the two inhibitors led to markedly different reprograming of the human kinome. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00134
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http://dx.doi.org/10.1021/acs.jproteome.9b00134DOI Listing
April 2019
1 Read

Mapping citrullinated sites in multiple organs of mice using hyper-citrullinated library.

J Proteome Res 2019 Apr 16. Epub 2019 Apr 16.

Protein citrullination (or deimination), irreversible post-translational modification, have been implicated in several physiological and pathological processes, including gene expression regulation, apoptosis, Rheumatoid arthritis, and Alzheimer's disease. Several researches have been carried out on citrullination in many conditions. However, until now, challenges in sample preparation and data analysis make it difficult to confidently identify a citrullinated protein and assign the citrullinated site. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00118DOI Listing
April 2019
2 Reads

TMT-based Quantitative Proteomics of Developing Sea Buckthorn Berries Reveals Candidate Proteins Related to Lipid Metabolism.

J Proteome Res 2019 Apr 16. Epub 2019 Apr 16.

Sea buckthorn (Hippophae L.) is an economically important shrub or small tree distributed in Eurasia. Most of the well-recognized medicinal and nutraceutical products are derived from its berry oil, which is rich in monounsaturated omega-7 (C16:1) fatty acid and polyunsaturated omega-6 (C18:2) and omega-3 (C18:3) fatty acids. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00764DOI Listing

Global quantification of intact proteins via chemical isotope labeling and mass spectrometry.

J Proteome Res 2019 Apr 16. Epub 2019 Apr 16.

Although thousands of intact proteins can be feasibly identified in recent years, global quantification of intact proteins is still challenging. Herein, we develop a high-throughput strategy for global intact protein quantification based on chemical isotope labeling. The isotope incorporation efficiency is as high as 99. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00071
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http://dx.doi.org/10.1021/acs.jproteome.9b00071DOI Listing
April 2019
1 Read

Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development.

J Proteome Res 2019 Apr 15. Epub 2019 Apr 15.

Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.

The condition of the placenta is a determinant of the short- and long-term health of the mother and the fetus. However, critical processes occurring in early placental development, such as trophoblast invasion and establishment of placental metabolism, remain poorly understood. To gain a better understanding of the genes involved in regulating these processes, we utilized a multiomics approach, incorporating transcriptome, proteome, and phosphoproteome data generated from mouse placental tissue collected at two critical developmental time points. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00970
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http://dx.doi.org/10.1021/acs.jproteome.8b00970DOI Listing
April 2019
1 Read

ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets.

J Proteome Res 2018 Dec 15;17(12):4227-4234. Epub 2018 Oct 15.

High-throughput tandem mass spectrometry has enabled the detection and identification of over 75% of all proteins predicted to result in translated gene products in the human genome. In fact, the galloping rate of data acquisition and sharing of mass spectrometry data has led to the current availability of many tens of terabytes of public data in thousands of human data sets. The systematic reanalysis of these public data sets has been used to build a community-scale spectral library of 2. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00496DOI Listing
December 2018

Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods.

J Proteome Res 2018 Dec;17(12):4023-4030

Institute for Systems Biology, Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics & School of Public Health, University of Michigan.

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http://dx.doi.org/10.1021/acs.jproteome.8b00885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288998PMC
December 2018

Enrichment of ATP binding proteins unveils proteomic alterations in human macrophage cell death, inflammatory response and protein synthesis after interaction with Candida albicans.

J Proteome Res 2019 Apr 15. Epub 2019 Apr 15.

Macrophages are involved in the primary human response to Candida albicans. After pathogen recognition signaling pathways are activated, leading to the production of cytokines, chemokines and antimicrobial peptides. ATP binding proteins are crucial for this regulation. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00032DOI Listing
April 2019
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Cost-Effective Automated Preparation of Serum Samples for Reproducible Quantitative Clinical Proteomics.

J Proteome Res 2019 Apr 15. Epub 2019 Apr 15.

Reproducible sample preparation remains a significant challenge in large-scale clinical research using selected reaction monitoring-mass spectrometry (SRM-MS), which enables a highly sensitive multiplexed assay. Although automated liquid handling platforms have tremendous potential for addressing this issue, the high cost of their consumables is a drawback that renders routine operation expensive. Here, we evaluated the performance of a liquid handling platform in preparing serum samples compared with a standard experiment while reducing the outlay for consumables, such as tips, wasted reagents, and reagent stock plates. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00023DOI Listing

A machine learning-based predictor of human-bacteria protein-protein interactions by incorporating comprehensive host network properties.

J Proteome Res 2019 Apr 15. Epub 2019 Apr 15.

Large-scale identification of protein-protein interactions (PPIs) between human and bacteria remains a crucial step to systematically understand the underlying molecular mechanisms of bacterial infection. Computational prediction approaches are playing an increasingly important role in accelerating the identification of PPIs. Here, we developed a new machine learning-based predictor of human-Yersinia pestis PPIs. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00074DOI Listing
April 2019
1 Read

Bias in False Discovery Rate Estimation in Mass-Spectrometry-Based Peptide Identification.

J Proteome Res 2019 Apr 18. Epub 2019 Apr 18.

Department of Data Analysis and Articial Intelligence, Faculty of Computer Science , National Research University Higher School of Economics (HSE) , 3 Kochnovskiy Proezd , Moscow 125319 , Russian Federation.

Accurate target-decoy-based false discovery rate (FDR) control of peptide identification from tandem mass-spectrometry data relies on an important but often neglected assumption that incorrect spectrum annotations are equally likely to receive either target or decoy peptides. Here we argue that this assumption is often violated in practice, even by popular methods. Preference can be given to target peptides by biased scoring functions, which result in liberal FDR estimations, or to decoy peptides by correlated spectra, which result in conservative estimations. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00991
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http://dx.doi.org/10.1021/acs.jproteome.8b00991DOI Listing
April 2019
1 Read

Serum Exosomes from Newborn Piglets Restrict Porcine Epidemic Diarrhea Virus Infection.

J Proteome Res 2019 Apr 17. Epub 2019 Apr 17.

State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Lanzhou , Gansu 730046 , China.

Exosomes are vehicles in the body fluid that participate in many biological processes, especially immune responses. In this study, we employed comparative proteome analysis to investigate the roles of serum exosomes during viral infection in neonates using porcine epidemic diarrhea virus (PEDV), a devastating enteric virus in newborn piglets, as a model virus. Serum exosomes were first isolated from newborn piglets infected with PEDV or mock-infected newborn piglets, followed by label-free LC-MS/MS-based comparative quantitative proteomic analysis. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00195DOI Listing

Mass spectrometry-based quantification of Tau in human cerebrospinal fluid using a complementary tryptic peptide standard.

J Proteome Res 2019 Apr 15. Epub 2019 Apr 15.

Here we report a method for the generation of complementary tryptic (CompTryp) isotope labeled peptide standards for the relative and absolute quantification of proteins by mass spectrometry (MS). These standards can be digested in parallel with either trypsin (Tryp-C) or trypsin-N (Tryp-N), to generate peptides that significantly overlap in primary sequence having C- and N-terminal arginine and lysine residues, respectively. As a proof of concept, an isotope-labeled CompTryp standard was synthesized for Tau, a well-established biomarker in Alzheimer's Disease (AD), which included both N- and C-terminal heavy isotope labeled (15N and 13C) arginine residues and flanking amino acid sequences to monitor proteolytic digestion. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00920DOI Listing

Integrated Tear Proteome and Metabolome Reveal Panels of Inflammatory-Related Molecules via Key Regulatory Pathways in Dry Eye Syndrome.

J Proteome Res 2019 Apr 16. Epub 2019 Apr 16.

Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College , Fudan University , Shanghai , China.

Dry eye syndrome (DES) is a growing public health concern with a high global prevalence; however, the fundamental processes involved in its pathogenic mechanisms remain poorly understood. In the present study, we applied nanoscale liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (nanoLC/Q-TOF-MS/MS) and ultraperformance LC/Q-TOF-MS/MS technologies on tear samples obtained from 18 dry eye patients and 19 healthy controls for integrated proteomic and metabolomic analyses. Overall, 1031 tear proteins were detected, while 190 proteins were determined to be significantly expressed in dry eye patients. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00149DOI Listing

Nuclear Magnetic Resonance Spectroscopy to Identify Metabolite Biomarkers of Nonresponsiveness to Targeted Therapy in Glioblastoma Tumor Stem Cells.

J Proteome Res 2019 Apr 18. Epub 2019 Apr 18.

Department of Chemistry , University of Oslo , Post Box 1033, Blindern NO-0315 , Oslo , Norway.

Glioblastoma is the most common and malignant brain tumor, and current therapies confer only modest survival benefits. A major obstacle is our ability to monitor treatment effect on tumors. Current imaging modalities are ambiguous, and repeated biopsies are not encouraged. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00801DOI Listing
April 2019
3 Reads

Mapping Post-Translational Modifications of de Novo Purine Biosynthetic Enzymes: Implications for Pathway Regulation.

J Proteome Res 2019 Apr 18. Epub 2019 Apr 18.

Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.

Purines represent a class of essential metabolites produced by the cell to maintain cellular homeostasis and facilitate cell proliferation. In times of high purine demand, the de novo purine biosynthetic pathway is activated; however, the mechanisms that facilitate this process are largely unknown. One plausible mechanism is through intracellular signaling, which results in enzymes within the pathway becoming post-translationally modified to enhance their individual enzyme activities and the overall pathway metabolic flux. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00969DOI Listing

Venom Composition in a Phenotypically Variable Pit Viper ( Trimeresurus insularis) across the Lesser Sunda Archipelago.

J Proteome Res 2019 Apr 17. Epub 2019 Apr 17.

School of Biological Sciences , University of Northern Colorado , 501 20th Street, CB 92 , Greeley , Colorado 80639-0017 , United States.

The genus Trimeresurus comprises a group of venomous pitvipers endemic to Southeast Asia and the Pacific Islands. Of these, Trimeresurus insularis, the White-lipped Island Pitviper, is a nocturnal, arboreal species that occurs on nearly every major island of the Lesser Sunda archipelago. In the current study, venom phenotypic characteristics of T. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00077
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http://dx.doi.org/10.1021/acs.jproteome.9b00077DOI Listing
April 2019
5 Reads

mineXpert: Biological Mass Spectrometry Data Visualization and Mining with Full JavaScript Ability.

Authors:
Filippo Rusconi

J Proteome Res 2019 Apr 17. Epub 2019 Apr 17.

LCP, UMR CNRS 8000, Université Paris-Sud , Université Paris Saclay , Build. 349 , 91400 Orsay , France.

Biological mass spectrometry mainly comprises three fields of endeavor, namely, proteomics, metabolomics, and structural biology. In each of these specialties, the mass spectrometrist needs to access MS mass spectral data, although not necessarily on the same basis. For example, the bottom-up proteomics scientist will occasionally access MS data to perform data inspection, quality assessments, and quantitation measurements, whereas top-down proteomics, structural biology, or metabolomics scientists will actually spend most of their time mining profile-mode MS data. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00099DOI Listing

Identification of 4-Hydroxyproline at the Xaa Position in Collagen by Mass Spectrometry.

J Proteome Res 2019 Apr 12. Epub 2019 Apr 12.

Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP) , University of Mons - UMONS , 23 Place du Parc , 7000 Mons , Belgium.

Collagen has a triple helix form, structured by a [-Gly-Xaa-Yaa-] repetition, where Xaa and Yaa are amino acids. This repeating unit can be post-translationally modified by enzymes, where proline is often hydroxylated into hydroxyproline (Hyp). Two Hyp isomers occur in collagen: 4-hydroxyproline (4Hyp, Gly-Xaa-Pro, substrate for 4-prolyl hydroxylase) and 3-hydroxyproline (3Hyp, Gly-Pro-4Hyp, substrate for 3-prolyl hydroxylase). Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00930
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http://dx.doi.org/10.1021/acs.jproteome.8b00930DOI Listing
April 2019
5 Reads

Mass Spectrometric Analysis of Lewy Body-Enriched α-Synuclein in Parkinson's Disease.

J Proteome Res 2019 Apr 15. Epub 2019 Apr 15.

Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry , Sahlgrenska Academy at the University of Gothenburg , S-431 80 Mölndal , Sweden.

Parkinson's disease (PD) is characterized by intraneuronal inclusions of aggregated α-synuclein protein (so-called Lewy bodies) in distinct brain regions. Multiple posttranslational modifications may affect the structure and function of α-synuclein. Mass spectrometry-based analysis may be useful for the characterization and quantitation of α-synuclein forms, but has proven challenging, mainly due to the insolubility of Lewy bodies in aqueous buffer. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00982DOI Listing
April 2019
2 Reads

QCQuan: A Web Tool for the Automated Assessment of Protein Expression and Data Quality of Labeled Mass Spectrometry Experiments.

J Proteome Res 2019 Apr 11. Epub 2019 Apr 11.

VITO NV , Applied Bio & molecular Systems , Boeretang 200 , Mol 2400 , Belgium.

In the context of omics disciplines and especially proteomics and biomarker discovery, the analysis of a clinical sample using label-based tandem mass spectrometry (MS) can be affected by sample preparation effects or by the measurement process itself, resulting in an incorrect outcome. Detection and correction of these mistakes using state-of-the-art methods based on mixed models can use large amounts of (computing) time. MS-based proteomics laboratories are high-throughput and need to avoid a bottleneck in their quantitative pipeline by quickly discriminating between high- and low-quality data. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00072DOI Listing
April 2019
1 Read

Obesity and Cage Environment Modulate Metabolism in the Zucker Rat: A Multiple Biological Matrix Approach to Characterizing Metabolic Phenomena.

J Proteome Res 2019 Apr 18. Epub 2019 Apr 18.

Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London , SW7 2AZ , United Kingdom.

Obesity and its comorbidities are increasing worldwide imposing a heavy socioeconomic burden. The effects of obesity on the metabolic profiles of tissues (liver, kidney, pancreas), urine, and the systemic circulation were investigated in the Zucker rat model using H NMR spectroscopy coupled to multivariate statistical analysis. The metabolic profiles of the obese ( fa/ fa) animals were clearly differentiated from the two phenotypically lean phenotypes, ((+/+) and ( fa/+)) within each biological compartment studied, and across all matrices combined. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00040DOI Listing
April 2019
1 Read

Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags while Significantly Reducing Instrument Time.

J Proteome Res 2019 Apr 12. Epub 2019 Apr 12.

Department of Molecular Genetics , University of Toronto , 1 King's College Circle , Toronto , ON , Canada M5S 1A8.

The balance between comprehensively analyzing the proteome and using valuable mass spectrometry time is a genuine challenge in the field of proteomics. Multidimensional fractionation strategies have significantly increased proteome coverage, but often at the cost of increased mass analysis time, despite advances in mass spectrometer acquisition rates. Recently, the Evosep One liquid chromatography system was shown to analyze peptide samples in a high-throughput manner without sacrificing in-depth proteomics coverage. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00082DOI Listing
April 2019
1 Read

Disordered Metabolic Profiling in Plasma and Tissues of Mice Infected with Artemisinin-Sensitive and -Resistant Plasmodium berghei K173 Determined by H NMR Spectroscopy.

J Proteome Res 2019 Apr 11. Epub 2019 Apr 11.

School of Pharmacy , Ningxia Medical University , Yinchuan 750004 , China.

Artemisinin resistance has inevitably emerged in several malaria-endemic areas and led to an incremental clinical failure rate for artemisinin-based combination therapy (ACT), which is strongly recommended by the World Health Organization (WHO). Genetically resilient malaria parasites have evolved antimalarial drug-evasion mechanisms; meanwhile, the metabolic cross-talk between the malaria parasites and the host is of significance during the invasion. The intention of this work, therefore, is to propose a feasible method to discover the systematic metabolic phenotypes of mice invaded with artemisinin-sensitive or -resistant Plasmodium berghei K173 when compared with healthy mice. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00782DOI Listing

A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis.

J Proteome Res 2019 Apr 10. Epub 2019 Apr 10.

Computational Systems Biochemistry , Max-Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany.

Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00927DOI Listing

Accurate Quantitative Proteomic Analyses Using Metabolic Labeling and High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS).

J Proteome Res 2019 Apr 17. Epub 2019 Apr 17.

Stable isotope labeling by amino acids in cell culture (SILAC) is routinely used to profile changes in protein and peptide abundance across different experimental paradigms. As with other quantitative proteomic approaches, the detection of peptide isotopomers can be limited by the presence of interference ions that ultimately affect the quality of quantitative measurements. Here, we evaluate high field asymmetric waveform ion mobility spectrometry (FAIMS) to improve the accuracy and dynamic range of quantitative proteomic analyses using SILAC. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00021DOI Listing

Tackling the Peak Overlap Issue in NMR Metabolomics Studies: 1D Projected Correlation Traces from Statistical Correlation Analysis on Nontilted 2D H NMR J-Resolved Spectra.

J Proteome Res 2019 Apr 8. Epub 2019 Apr 8.

CIBION-CONICET, Centro de Investigaciones en Bionanociencias , NMR Group , Polo Científico Tecnológico , Ciudad Autónoma de Buenos Aires C1425FQD , Argentina.

The identification of metabolites in complex biological matrices is a challenging task in 1D H-NMR-based metabolomics studies. Statistical total correlation spectroscopy (STOCSY) has emerged for aiding the structural elucidation by revealing the peaks that present a high correlation to a driver peak of interest (which would likely belong to the same molecule). However, in these studies, the signals from metabolites are normally present as a mixture of overlapping resonances, limiting the performance of STOCSY. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00093DOI Listing

Mitochondrial Function, Metabolic Regulation, and Human Disease Viewed through the Prism of Sirtuin 4 (SIRT4) Functions.

J Proteome Res 2019 Apr 8. Epub 2019 Apr 8.

Department of Molecular Biology , Princeton University , Princeton , New Jersey 08544 , United States.

As cellular metabolic hubs, mitochondria are the main energy producers for the cell. These organelles host essential energy producing biochemical processes, including the TCA cycle, fatty acid oxidation, and oxidative phosphorylation. An accumulating body of literature has demonstrated that a majority of mitochondrial proteins are decorated with diverse posttranslational modifications (PTMs). Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00086
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http://dx.doi.org/10.1021/acs.jproteome.9b00086DOI Listing
April 2019
4 Reads

Alterations of Human Plasma Proteome Profile on Adaptation to High-Altitude Hypobaric Hypoxia.

J Proteome Res 2019 Apr 3. Epub 2019 Apr 3.

Institute of Blood Transfusion , Chinese Academy of Medical Sciences & Peking Union Medical College , Chengdu 610052 , China.

For individuals migrating to or residing permanently in high-altitude regions, environmental hypobaric hypoxia is a primary challenge that induces several physiological or pathological responses. It is well documented that human beings adapt to hypobaric hypoxia via some protective mechanisms, such as erythropoiesis and overproduction of hemoglobin; however, little is known on the alterations of plasma proteome profiles in accommodation to high-altitude hypobaric hypoxia. In the present study, we investigated differential plasma proteomes of high altitude natives and lowland normal controls by a TMT-based proteomic approach. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00911DOI Listing

Targeted Quantitative Kinome Analysis Identifies PRPS2 as a Promoter for Colorectal Cancer Metastasis.

J Proteome Res 2019 Apr 2. Epub 2019 Apr 2.

Department of Chemistry , University of California , Riverside , California 92521-0403 , United States.

Kinases are among the most important families of enzymes involved in cell signaling. In this study, we employed a recently developed parallel-reaction monitoring (PRM)-based targeted proteomic method to examine the reprogramming of the human kinome during colorectal cancer (CRC) metastasis. We were able to quantify the relative expression of 299 kinase proteins in a pair of matched primary/metastatic CRC cell lines. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00119DOI Listing

Analysis of Single-Nucleotide Polymorphisms in Human Voltage-Gated Ion Channels.

J Proteome Res 2019 Apr 1. Epub 2019 Apr 1.

Section of Cell Biology and Biophysics, Department of Biology, School of Sciences , National and Kapodistrian University of Athens , Panepistimiopolis, Athens 15701 , Greece.

Voltage-gated ion channels (VGICs) are one of the largest groups of transmembrane proteins. Due to their major role in the generation and propagation of electrical signals, VGICs are considered important from a medical viewpoint, and their dysfunction is often associated with Channelopathies. We identified disease-associated mutations and polymorphisms in these proteins through mapping missense single-nucleotide polymorphisms from the UniProt and ClinVar databases on their amino acid sequence, considering their special topological and functional characteristics. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00121DOI Listing
April 2019
4.245 Impact Factor

A Large-Scale, Multi-Center Urine Biomarkers Identification of Coronary Heart Disease in TCM Syndrome Differentiation.

J Proteome Res 2019 Apr 9. Epub 2019 Apr 9.

Tianjin University of Traditional Chinese Medicine , Tianjin 300193 , China.

Coronary heart disease (CHD) threatens human health. The discovery and assessment of potential biometabolic markers for different syndrome types of CHD may contribute to decipher pathophysiological mechanisms and identify new targets for diagnosis and treatment. On the basis of UPLC-Q-TOF/MS metabolomics technology, urine samples of 1072 participants from nine centers, including normal control, phlegm and blood stasis (PBS) syndrome and Qi and Yin deficiency (QYD) syndrome, and other syndromes of CHD, were conducted to find biomarkers. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00799DOI Listing
April 2019
1 Read
4.245 Impact Factor

Significant Down-Regulation of Urea Cycle Generates Clinically Relevant Proteomic Signature in Hepatocellular Carcinoma Patients with Macrovascular Invasion.

J Proteome Res 2019 Mar 29. Epub 2019 Mar 29.

Jiangsu Key Laboratory of Molecular Medicine , Medical School of Nanjing University , 22 Hankou Road , Gulou District, Nanjing 210093 , China.

Vascular invasion is considered as the critical risk factor of hepatocellular carcinoma (HCC). To reveal the molecular mechanisms underlying macrovascular invasion (MaVI) in HCC, we performed an iTRAQ based proteomic study to identify notably dysregulated proteins from eight HCC patients with differential vascular invasion and further confirmed them in the other 53 HCC patients. Forty-seven proteins were found significantly down-regulated in HCC with MaVI. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00921
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http://dx.doi.org/10.1021/acs.jproteome.8b00921DOI Listing
March 2019
4 Reads

Untargeted Metabolomics Differentiates l-Carnitine Treated Septic Shock 1-Year Survivors and Nonsurvivors.

J Proteome Res 2019 Apr 1. Epub 2019 Apr 1.

Emergency Medicine , University of Mississippi Medical Center , Jackson , Mississippi 39216 , United States.

l-Carnitine is a candidate therapeutic for the treatment of septic shock, a condition that carries a ≥40% mortality. Responsiveness to l-carnitine may hinge on unique metabolic profiles that are not evident from the clinical phenotype. To define these profiles, we performed an untargeted metabolomic analysis of serum from 21 male sepsis patients enrolled in a placebo-controlled l-carnitine clinical trial. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00774DOI Listing
April 2019
2 Reads

Evaluation and Optimization of Sample Handling Methods for Quantification of Short-Chain Fatty Acids in Human Fecal Samples by GC-MS.

J Proteome Res 2019 Apr 1. Epub 2019 Apr 1.

School of Pharmacy, College of Medicine , National Taiwan University , Taipei City , Taiwan.

The gut microbiota has attracted a great deal of interest in recent years due to its association with many diseases. Short-chain fatty acids (SCFAs), the end products of dietary fiber fermentation by the intestinal microbiota, are among the most frequently discussed gut metabolites. As the sample handling method greatly affects the integrity of data, this study investigated the most important parameters that affect the bias of SCFA comparisons in human fecal studies. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00536
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http://dx.doi.org/10.1021/acs.jproteome.8b00536DOI Listing
April 2019
6 Reads

Time Series Characteristics of Serum Branched-Chain Amino Acids for Early Diagnosis of Chronic Heart Failure.

J Proteome Res 2019 Mar 29. Epub 2019 Mar 29.

Key Laboratory of Drug Quality Control and Pharmacovigilance , China Pharmaceutical University, Ministry of Education , Nanjing 210009 , China.

Chronic heart failure (CHF) is an ongoing clinical syndrome with cardiac dysfunction that can be traced to alterations in cardiac metabolism. The identification of metabolic biomarkers in easily accessible fluids to improve the early diagnosis of CHF has been elusive to date. In this study, we took multidimensional analytical techniques to discover potentially new diagnostic biomarkers by focusing on the dynamic changes of metabolites in serum during the progression of CHF. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00002DOI Listing
March 2019
2 Reads

Serum Metabolomics Study of Nonsmoking Female Patients with Non-Small Cell Lung Cancer Using Gas Chromatography-Mass Spectrometry.

J Proteome Res 2019 Mar 29. Epub 2019 Mar 29.

CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China.

The incidence of nonsmoking female patients with non-small cell lung cancer (NSCLC) has increased in recent decades; however, the pathogenesis of patients is unclear, and early diagnosis biomarkers are in urgent need. In this study, 136 nonsmoking female subjects (65 patients with NSCLC, 6 patients with benign lung tumors, and 65 healthy controls) were enrolled, and their metabolic profiling was investigated by using pseudotargeted gas chromatography-mass spectrometry. A total of 56 annotated metabolites were found and verified to be significantly different in nonsmoking females with NSCLC compared with the control. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00069DOI Listing
March 2019
4 Reads
4.245 Impact Factor

Proteomic Analysis of Human Plasma during Intermittent Fasting.

J Proteome Res 2019 Apr 1. Epub 2019 Apr 1.

Charles Perkins Centre, School of Life and Environmental Sciences , University of Sydney , Sydney , NSW 2006 , Australia.

Intermittent fasting (IF) increases lifespan and decreases metabolic disease phenotypes and cancer risk in model organisms, but the health benefits of IF in humans are less clear. Human plasma derived from clinical trials is one of the most difficult sample sets to analyze using mass spectrometry-based proteomics due to the extensive sample preparation required and the need to process many samples to achieve statistical significance. Here, we describe an optimized and accessible device (Spin96) to accommodate up to 96 StageTips, a widely used sample preparation medium enabling efficient and consistent processing of samples prior to LC-MS/MS. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00090
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http://dx.doi.org/10.1021/acs.jproteome.9b00090DOI Listing
April 2019
4 Reads

Comprehensive N-Glycome Profiling of Cells and Tissues for Breast Cancer Diagnosis.

J Proteome Res 2019 Apr 2. Epub 2019 Apr 2.

Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology , Ocean University of China , Qingdao 266003 , China.

Aberrant protein glycosylation is observed in the progression of many types of diseases, including different cancers. In this study, we assess differential N-glycan patterns of human breast cancer cells and tissues by PGC-ESI-MS/MS. Compared with mammary epithelial cells, high-mannose glycans were significantly elevated in breast cancer cells. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00073DOI Listing
April 2019
4.245 Impact Factor

Metabolic Profiling of Tumors, Sera, and Skeletal Muscles from an Orthotopic Murine Model of Gastric Cancer Associated-Cachexia.

J Proteome Res 2019 Apr 27;18(4):1880-1892. Epub 2019 Mar 27.

Department of Physical Education , Xiamen University of Technology , Xiamen 361005 , China.

Cachexia is a complex metabolic derangement syndrome that affects approximately 50-80% of cancer patients. So far, few works have been reported to provide a global overview of gastric cancer cachexia (GCC)-related metabolic changes. We established a GCC murine model by orthotopicly implanting BGC823 cell line and conducted NMR-based metabolomic analysis of gastric tissues, sera, and gastrocnemius. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00088
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http://dx.doi.org/10.1021/acs.jproteome.9b00088DOI Listing
April 2019
14 Reads

An unbiased lipid phenotyping approach to study the genetic determinants of lipids and their association with coronary heart disease risk factors.

J Proteome Res 2019 Mar 19. Epub 2019 Mar 19.

Background: Studies of the association of lipids with coronary heart disease (CHD) have predominantly assessed major lipid markers, but scientific understanding of individual lipids, underlying metabolic pathways, and their genetic determinants is limited. Direct infusion high-resolution mass spectrometry (DIHRMS) is a novel, high-throughput approach to rapidly and accurately profile hundreds of lipids in human serum without prior chromatography, allowing rapid and detailed lipid phenotyping for large epidemiological studies to provide insight about the association of lipids with CHD risk factors.

Methods: Intact lipid profiling by DIHRMS was performed on 5,662 serum samples from healthy participants in the Pakistan Risk of Myocardial Infarction Study (PROMIS). Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00786
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http://dx.doi.org/10.1021/acs.jproteome.8b00786DOI Listing
March 2019
3 Reads
4.245 Impact Factor

Evaluating Chromatographic Approaches for the Quantitative Analysis of a Human Proteome on Orbitrap-Based Mass Spectrometry Systems.

J Proteome Res 2019 Apr 27;18(4):1857-1869. Epub 2019 Mar 27.

Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States.

The Orbitrap is now a core component of several different instruments. However, evaluating the capabilities of each system is lacking in the field. Here, we compared the performance of multidimensional protein identification (MudPIT) on Velos Pro Orbitrap and Velos Orbitrap Elite mass spectrometers to reversed phase liquid chromatography (RPLC) on a Q-Exactive Plus and an Orbitrap Fusion Lumos. Read More

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http://dx.doi.org/10.1021/acs.jproteome.9b00036DOI Listing

Functional Insights from the Proteomic Inventory of Ovine Forestomach Matrix.

J Proteome Res 2019 Apr 25;18(4):1657-1668. Epub 2019 Mar 25.

Aroa Biosurgery Limited , Airport Oaks , Auckland 2022 , New Zealand.

Ovine forestomach matrix (OFM) is a decellularized extracellular matrix (dECM) biomaterial that serves as a scaffold for remodeling damaged soft tissue. dECM biomaterials are used in a variety of clinical applications, and their regenerative capacity is encoded not only in their biophysical properties but also in their molecular diversity. In this study, the proteome of OFM was characterized via both targeted and global mass spectrometry (MS) with the use of heavy isotope labeled (SIL) internal standards. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00908DOI Listing

One-Step SH2 Superbinder-Based Approach for Sensitive Analysis of Tyrosine Phosphoproteome.

J Proteome Res 2019 Apr 25;18(4):1870-1879. Epub 2019 Mar 25.

CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China.

Tyrosine phosphorylation plays a major role in regulating cell signaling pathways governing diverse biological functions such as proliferation and differentiation. Systemically mapping phosphotyrosine (pTyr) sites is the key to understanding molecular mechanisms underlining pTyr-dependent signaling. Although mass spectrometry-based technologies have been widely used for pTyr site profiling and quantification, their applications are often hindered by the poor efficiency in current multistep enrichment procedures for inherently low abundance pTyr peptides, especially under physiological conditions. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00045
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http://dx.doi.org/10.1021/acs.jproteome.9b00045DOI Listing
April 2019
5 Reads

Identification of the Direct Substrates of the ABL Kinase via Kinase Assay Linked Phosphoproteomics with Multiple Drug Treatments.

J Proteome Res 2019 Apr 21;18(4):1679-1690. Epub 2019 Mar 21.

Ableson tyrosine kinase (ABL) plays essential roles in cell differentiation, division, adhesion, and stress response. However, fusion of the breakpoint cluster region (BCR) to ABL produces constitutive kinase activity that causes chronic myelogenous leukemia (CML). Small molecule tyrosine kinase inhibitors (TKIs) such as imatinib revolutionized the treatment of CML and other cancers, but acquired resistance to these inhibitors is rising. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00942
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http://dx.doi.org/10.1021/acs.jproteome.8b00942DOI Listing
April 2019
4 Reads

Quantitative Proteomics Combined with Affinity MS Revealed the Molecular Mechanism of Ginsenoside Antitumor Effects.

J Proteome Res 2019 Mar 29. Epub 2019 Mar 29.

State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Haihe Education Park, 38 Tongyan Road , Tianjin 300353 , People's Republic of China.

Ginsenosides have previously been demonstrated to effectively inhibit cancer cell growth and survival in both animal models and cell lines. However, the specific ginsenoside component that is the active ingredient for cancer treatment through interaction with a target protein remains unknown. By an integrated quantitative proteomics approach via affinity mass spectrum (MS) technology, we deciphered the core structure of the ginsenoside active ingredient derived from crude extracts of ginsenosides and progressed toward identifying the target protein that mediates its anticancer activity. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00972DOI Listing

Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.

J Proteome Res 2019 Apr 22;18(4):1477-1485. Epub 2019 Mar 22.

Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.

Label-free quantification has become a common-practice in many mass spectrometry-based proteomics experiments. In recent years, we and others have shown that spectral clustering can considerably improve the analysis of (primarily large-scale) proteomics data sets. Here we show that spectral clustering can be used to infer additional peptide-spectrum matches and improve the quality of label-free quantitative proteomics data in data sets also containing only tens of MS runs. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00377
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http://dx.doi.org/10.1021/acs.jproteome.8b00377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456873PMC
April 2019
7 Reads

IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments.

J Proteome Res 2019 Apr 20;18(4):1751-1759. Epub 2019 Mar 20.

Department for Biochemistry and Molecular Biology , University of Southern Denmark , Campusvej 55 , 5230 Odense , Denmark.

Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operations to ensure tool interoperability. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00968
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http://dx.doi.org/10.1021/acs.jproteome.8b00968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456869PMC
April 2019
7 Reads

Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery.

J Proteome Res 2019 Apr 21;18(4):1907-1915. Epub 2019 Mar 21.

J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States.

Clinical biomarkers identified by shotgun proteomics require proteins in body fluids or tissues to be enzymatically digested before being separated and sequenced by liquid chromatography-tandem mass spectrometry. How well peptide signals can be resolved and detected is largely dependent on the quality of sample preparation. Conventional approaches such as in-gel, in-solution, and filter-based digestion, despite their extensive implementation by the community, become less appealing due to their unsatisfying protein/peptide recovery rate, lengthy sample processing, and/or lowcost-effectiveness. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00037
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http://dx.doi.org/10.1021/acs.jproteome.9b00037DOI Listing
April 2019
8 Reads
4.245 Impact Factor