Abstract：
:Prostate cancer (PCa) is the second leading cause of cancer-related mortality in men. The prevalent diagnosis method is based on the serum prostate-specific antigen (PSA) screening test, which suffers from low specificity, overdiagnosis, and overtreatment. In this work, untargeted metabolomic profiling of age-matched serum samples from prostate cancer patients and healthy individuals was performed using ultraperformance liquid chromatography coupled to high-resolution tandem mass spectrometry (UPLC-MS/MS) and machine learning methods. A metabolite-based in vitro diagnostic multivariate index assay (IVDMIA) was developed to predict the presence of PCa in serum samples with high classification sensitivity, specificity, and accuracy. A panel of 40 metabolic spectral features was found to be differential with 92.1% sensitivity, 94.3% specificity, and 93.0% accuracy. The performance of the IVDMIA was higher than the prevalent PSA test. Within the discriminant panel, 31 metabolites were identified by MS and MS/MS, with 10 further confirmed chromatographically by standards. Numerous discriminant metabolites were mapped in the steroid hormone biosynthesis pathway. The identification of fatty acids, amino acids, lysophospholipids, and bile acids provided further insights into the metabolic alterations associated with the disease. With additional work, the results presented here show great potential toward implementation in clinical settings.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Zang X,Jones CM,Long TQ,Monge ME,Zhou M,Walker LD,Mezencev R,Gray A,McDonald JF,Fernández FMdoi
10.1021/pr500409qsubject
Has Abstractpub_date
2014-07-03 00:00:00pages
3444-54issue
7eissn
1535-3893issn
1535-3907journal_volume
13pub_type
杂志文章abstract：:We describe Peptoonist, a program that can automatically identify the glycans (sugars) present at each N-glycosylation site of a protein. The input to Peptoonist is a series of mass spectra, both MS and MS/MS, obtained from a liquid chromatography (LC) run of proteolytically digested purified glycoproteins. The progra...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070239f
更新日期：2007-10-01 00:00:00
abstract：:In this paper, we describe a method for analyzing large-volume protein samples using capillary electrophoresis in conjunction with laser-induced fluorescence detection (CE-LIF). To improve the stacking and separation efficiencies of proteins, we added either 0.01% sodium dodecyl sulfate (SDS) or 0.01% poly(ethylene ox...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050298y
更新日期：2006-02-01 00:00:00
abstract：:Populus tremula L. x P. alba L. (Populus x canescens (Aiton) Smith), clone INRA 717-1-B4, saplings were subjected to 120 ppb ozone exposure for 28 days. Chloroplasts were isolated, and the membrane proteins, solubilized using the detergent 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), were analyzed in a differen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1012009
更新日期：2011-07-01 00:00:00
abstract：:Adipose tissue is a major storage site for lipophilic environmental contaminants. The environmental metabolic disruptor hypothesis postulates that some pollutants can promote obesity or metabolic disorders by activating nuclear receptors involved in the control of energetic homeostasis. In this context, monoethylhexyl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200765v
更新日期：2011-12-02 00:00:00
abstract：:Mutagenesis through fast neutron (FN) radiation of soybean resulted in a mutant with a 15% increase in seed protein content. A comparative genomic hybridization analysis confirmed that the mutant is lacking 24 genes located at chromosomes 5 and 10. A tandem mass tag-based proteomic profiling of the wild type and the F...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00160
更新日期：2020-10-02 00:00:00
abstract：:Ricin is a type II ribosome-inactivating protein toxin consisting of A and B chains linked by one interchain disulfide bond. Because of its high toxicity depending on both chains together, confirming the presence of both A and B chains of intact ricin is required during the investigation of the illegal production and ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00458
更新日期：2021-01-01 00:00:00
abstract：:The effects of acute and chronic stress on the production of systemic metabolites were investigated in male Sprague-Dawley (SD) rats. Metabolites excreted in urine were analyzed using GC/MS in conjunction with multivariate and univariate statistical techniques. SD rats were subjected to two kinds of acute stress and c...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr801086k
更新日期：2009-05-01 00:00:00
abstract：:Major depressive disorder (MDD) is a socially detrimental psychiatric disorder, contributing to increased healthcare expenditures and suicide rates. However, no empirical laboratory-based tests are available to support the diagnosis of MDD. In this study, a NMR-based plasma metabonomic method for the diagnosis of MDD ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2010082
更新日期：2012-03-02 00:00:00
abstract：:We analyzed a unique rice (Oryza sativa L.) blast lesion mimic (blm) mutant for differentially expressed proteins in leaves of one- and two-week-old seedlings manifesting the lesion mimic phenotype. Gel-based one- and two-dimensional electrophoresis (1- and 2-DGE) was performed using leaves (blm and wild-type, WT) bef...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060092c
更新日期：2006-10-01 00:00:00
abstract：:In humans, the olfactory epithelium is located in two narrow passages, the olfactory clefts, at the upper part of the nasal cavities. The olfactory epithelium is covered by a mucus layer which is essential for the function of the olfactory neurons that are directly connected with the brain through the cribriform plate...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0606575
更新日期：2007-05-01 00:00:00
abstract：:Catechol estrogens (CEs) are known to be toxic metabolites and the initiators of the oncogenesis of breast cancers via forming covalent adducts with DNAs. CEs shall also react with proteins, but their cellular protein targets remain unexplored. Here, we reported the identification of protein targets of CEs in the solu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00578
更新日期：2021-01-01 00:00:00
abstract：:Almond, as a part of the nut family, is an important source of biological compounds, and specifically, almond skins have been considered an important source of polyphenols, including flavan-3-ols and flavonols. Polyphenol metabolism may produce several classes of metabolites that could often be more biologically activ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100639v
更新日期：2010-11-05 00:00:00
abstract：:In pressure overload (PO), sex differences in humans and rodents have been well documented and estrogen receptor (ER) β is considered cardioprotective. However, the underlying mechanisms are poorly understood. Our aim was to investigate sex- and ERβ-specific effects in protein abundance in PO employing a 2-dimensional...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500749j
更新日期：2014-12-05 00:00:00
abstract：:Epithelial cells play an important role in physiological and pathophysiological situations, with organ-, tissue-, type-, and function-specific patterns. Proteome analysis has been used to study epithelial-origin diseases and identify novel prognostic, diagnostic, and therapeutic markers. The present review compares th...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr050389v
更新日期：2006-04-01 00:00:00
abstract：:Colorectal cancer (CRC) is the third most common cancer worldwide and has poor prognosis. To identify the proteins involved in colorectal carcinogenesis, we employed 2-DE and MALDI-TOF/TOF-based proteomics approach to study the differentially expressed proteins in tumor and adjacent nontumor tissue samples. Samples fr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900365e
更新日期：2009-10-01 00:00:00
abstract：:Streptococcus agalactiae causes severe systemic infections in human and fish. In the present study, we established a pathogen-plasma interaction model by which we explored how S. agalactiae evaded serum-mediated killing. We found that S. agalactiae grew faster in the presence of yellow grouper plasma than in the absen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00215
更新日期：2016-07-01 00:00:00
abstract：: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.g., with affi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00927
更新日期：2019-05-03 00:00:00
abstract：:Ureteral obstruction will lead clinically to hydronephrosis, which may further develop into partial or complete loss of kidney function and even cause permanent histological damage. However, there is little knowledge of metabolic responses during the obstructed process and its recoverability. In this study, a complete...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00304
更新日期：2018-09-07 00:00:00
abstract：:While numerous strategies exist for biomarker discovery, the bottleneck to product development and routine use at the clinic is in the verification phase of candidate biomarkers. The aim of this study was to establish a robust and high-throughput product ion monitoring (PIM) assay that is potentially capable of rapidl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7005999
更新日期：2008-02-01 00:00:00
abstract：:Chinese hamster ovary (CHO) cell lines are widely used for the expression of therapeutic recombinant proteins, including monoclonal antibodies and other biologics. For manufacturing, cells derived from a single-cell clone are typically used to ensure product consistency. Presently, fetal bovine serum (FBS) is commonly...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400352n
更新日期：2013-07-05 00:00:00
abstract：:Proteomics has been applied to study intracellular bacteria and phagocytic vacuoles in different host cell lines, especially macrophages (Mφs). For mycobacterial phagosomes, few studies have identified over several hundred proteins for systems assessment of the phagosome maturation and antigen presentation pathways. M...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101245u
更新日期：2011-05-06 00:00:00
abstract：:The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked wit...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00370
更新日期：2017-12-01 00:00:00
abstract：:In type-1 diabetes mellitus (T1DM) with diabetic nephropathy (DN), accumulation of abnormal proteins in the kidney and other tissues may derive from constitutive alterations of intracellular protein recognition, assembly, and turnover. We characterized the proteins involved in these functions in cultured skin fibrobla...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060443n
更新日期：2007-03-01 00:00:00
abstract：:Methotrexate (MTX) is a chemotherapeutic agent that can cause a range of toxic side effects including gastrointestinal damage, hepatotoxicity, myelosuppression, and nephrotoxicity and has potentially complex interactions with the gut microbiome. Following untargeted UPLC-qtof-MS analysis of urine and fecal samples fro...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00230
更新日期：2020-08-07 00:00:00
abstract：:The Biology/Disease-driven (B/D) working groups of the Human Proteome Project are alliances of research groups aimed at developing or improving proteomic tools to support specific biological or disease-related research areas. Here, we describe the activities and progress to date of the B/D working group focused on pro...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.8b00401
更新日期：2018-12-07 00:00:00
abstract：:Oxidative stress and inflammation play a role in the physiopathology of insulin resistance, diabetes and cardiovascular disease. A single high-fat, high-carbohydrate (HFHC) meal induces an increase in inflammatory and oxidative stress markers in peripheral blood mononuclear cells (PBMC). Previous studies have shown th...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00476
更新日期：2017-11-03 00:00:00
abstract：:New technologies have advanced the field of proteomics, and a number of companies have developed innovative platforms to drive this research. However, significant challenges are often encountered when trying to integrate complementary technologies from multiple manufacturers. We have developed a software and hardware ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050465u
更新日期：2006-09-01 00:00:00
abstract：:Completion of the human genome sequence has provided scientists with powerful resources with which to explore the molecular events associated with disease states such as diabetes. Understanding the relative levels of expression of gene products, especially of proteins, and their post-translational modifications will b...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050024a
更新日期：2005-05-01 00:00:00
abstract：:Carcinoma, the most common type of cancer, arises from epithelial cells. The transition from adenoma to carcinoma is associated with the loss of E-cadherin and, in consequence, the disruption of cell-cell contacts. E-cadherin is a tumor suppressor, and it is down-regulated during epithelial-to-mesenchymal transition (...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00046
更新日期：2017-08-04 00:00:00
abstract：:The skin is the primary boundary between the body and the environment. In addition to its properties as a physical barrier, skin keratinocytes actively participate in many defense mechanisms. Viral double-stranded RNA (dsRNA) is the most important viral structure involved in activation of immune response. Intracellula...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr901040u
更新日期：2010-03-05 00:00:00
