Abstract：
:Plasma biomarkers of exposure to environmental contaminants play an important role in early detection of disease. The emerging field of proteomics presents an attractive opportunity for candidate biomarker discovery, as it simultaneously measures and analyzes a large number of proteins. This article presents a case study for measuring arsenic concentrations in a population residing in an As-endemic region of Bangladesh using plasma protein expressions measured by SELDI-TOF mass spectrometry. We analyze the data using a unified statistical method based on functional learning to preprocess mass spectra and extract mass spectrometry (MS) features and to associate the selected MS features with arsenic exposure measurements. The task is challenging due to several factors, the high dimensionality of mass spectrometry data, complicated error structures, and a multiple comparison problem. We use nonparametric functional regression techniques for MS modeling, peak detection based on the significant zero-downcrossing method, and peak alignment using a warping algorithm. Our results show significant associations of arsenic exposure to either under- or overexpressions of 20 proteins.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Harezlak J,Wu MC,Wang M,Schwartzman A,Christiani DC,Lin Xdoi
10.1021/pr070491nsubject
Has Abstractpub_date
2008-01-01 00:00:00pages
217-24issue
1eissn
1535-3893issn
1535-3907journal_volume
7pub_type
杂志文章abstract：:Aspergillus fumigatus is a ubiquitously distributed filamentous fungus that has emerged as one of the most serious life-threatening pathogens in immunocompromised patients. The mechanisms for its pathogenicity are poorly understood. Here, we analyzed the proteome of dormant A. fumigatus conidia as the fungal entity ha...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr9010684
更新日期：2010-07-02 00:00:00
abstract：:The nation-wide electronic health record database acts as an interoperable repository of health data obtained throughout citizen contacts with health care providers. This system improves accessibility for citizens and researchers to health data with the ability to assign context to disease development. In that system,...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1007784
更新日期：2011-01-07 00:00:00
abstract：:FDA oversight of medical devices, including in vitro diagnostic devices (IVDs or laboratory tests), in the United States was a direct result of the passage of the Medical Device Amendments of 1976. This law introduced a series of general controls for medical devices including registration and listing, requirements for...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr050059a
更新日期：2005-07-01 00:00:00
abstract：:The peptide toxins in the venoms of small invertebrates such as stinging ants have rarely been studied due to the limited amount of venom available per individual. We used a venomics strategy to identify the molecular diversity of the venom peptidome for the myrmicine ant Tetramorium bicarinatum. The methodology inclu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00452
更新日期：2018-10-05 00:00:00
abstract：:Controlled ovarian hyperstimulation is performed to assist with generation of multiple mature oocytes for use in in vitro fertilization (IVF). The goal of our study was to evaluate differences in protein and steroid profiles in ovarian follicular fluid (hFF) samples obtained during oocyte retrieval from women undergoi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300535g
更新日期：2012-10-05 00:00:00
abstract：:In recent years, proteomic data have contributed to genome annotation efforts, most notably in humans and mice, and spawned a field termed "proteogenomics". Yeast, in contrast with higher eukaryotes, has a small genome, which has lent itself to simpler ORF prediction. Despite this, continual advances in mass spectrome...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00734
更新日期：2015-12-04 00:00:00
abstract：:We undertook an unbiased metabolite profiling of fibroblasts from schizophrenia patients and healthy controls to identify metabolites and pathways that are dysregulated in disease, seeking to gain new insights into the disease biology of schizophrenia and to discover potential disease-related biomarkers. We measured p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00628
更新日期：2017-02-03 00:00:00
abstract：:The present study was undertaken to identify proteins interacting with PrP(C) that could provide new insights into its physiological functions and pathological role. Human PrP(C) was expressed in prion protein-deficient murine hippocampus (HpL3-4) neuronal cells. The PrP(C) along with its interacting proteins were aff...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2001989
更新日期：2011-07-01 00:00:00
abstract：:Growing appreciation for astrocytes as active participants in nervous system development, neurovascular metabolic coupling, and neurological disease progression has stimulated recent investigation into specific astrocyte-secreted proteins that may mediate these functions. The current work utilized SILAC-generated isot...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100134n
更新日期：2010-05-07 00:00:00
abstract：:The plasma of patients with stable carotid atherosclerosis (n = 9), and healthy subjects (n = 10) have been fingerprinted with both GC-MS and (1)H NMR. Principal component analysis (PCA), partial least-squares-discriminant analysis (PLS-DA) and orthogonal partial least-squares-discriminant analysis (OPLS-DA) have been...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900668v
更新日期：2009-12-01 00:00:00
abstract：:Two-dimensional differential gel electrophoresis (2-D DIGE) was used to analyze human serum following the removal of albumin and five other high-abundant serum proteins. After protein removal, serum was analyzed by SDS-PAGE as a preliminary screen, and significant differences between four high-abundant protein removal...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049921p
更新日期：2004-11-01 00:00:00
abstract：:The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyse...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900663d
更新日期：2009-11-01 00:00:00
abstract：:Bacillus weihenstephanensis is a subspecies of the Bacillus cereus sensu lato group of spore-forming bacteria known to cause food spoilage or food poisoning. The key distinguishing phenotype of B. weihenstephanensis is its ability to grow below 7 °C or, from a food safety perspective, to grow and potentially produce t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501307t
更新日期：2015-05-01 00:00:00
abstract：:The term "spectral clustering" is sometimes used to refer to the clustering of mass spectrometry data. However, it also classically refers to a family of popular clustering algorithms. To avoid confusion, a more specific term could advantageously be coined. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00516
更新日期：2019-01-04 00:00:00
abstract：:Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG repeat within the Huntingtin (HTT) gene, though the clinical presentation of disease and age-of-onset are strongly influenced by ill-defined environmental factors. We recently reported a gene-environment interaction wherein expressi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200839d
更新日期：2012-02-03 00:00:00
abstract：:Glutaredoxins (GRXs), small redox proteins that use reduced glutathione as an electron donor, are key components of the cellular antioxidant system. In this study, we used Saccharomyces cerevisiae as a model system to investigate the effects of GRX deletion on yeast chronological life span (CLS). Deletion of either Gr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00012
更新日期：2018-07-06 00:00:00
abstract：:Major depressive disorder (MDD) is a debilitating mental disease with a pronounced impact on the quality of life of many people; however, it is still difficult to diagnose MDD accurately. In this study, a nontargeted metabolomics approach based on ultra-high-performance liquid chromatography equipped with quadrupole t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00144
更新日期：2015-05-01 00:00:00
abstract：:The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00703
更新日期：2018-03-02 00:00:00
abstract：:Histones regulate a variety of chromatin templated events by their post-translational modifications (PTMs). Although there are extensive reports on the PTMs of canonical histones, the information on the histone variants remains very scanty. Here, we report the identification of different PTMs, such as acetylation, met...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500597a
更新日期：2014-12-05 00:00:00
abstract：:Salt stress is a major abiotic factor limiting maize yield. To characterize the mechanism underlying maize salt tolerance, we compared the seedling root proteomes of salt-tolerant Jing724 and salt-sensitive D9H. The germination rate and growth parameter values (weight and length) were higher for Jing724 than for D9H u...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00455
更新日期：2018-01-05 00:00:00
abstract：:Influenza A virus (IAV) is a major human pathogen whose genotypic diversity results in unpredictable pandemics and epidemics. Interaction with the cell nucleus is essential to IAV infection, allowing recruitment of cellular components to facilitate virus replication. Viral proteins are also targeted to the nucleolus, ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100593g
更新日期：2010-10-01 00:00:00
abstract：:Decoy database searches are used to filter out false positive protein identifications derived from search engines, but there is no consensus about which decoy is "the best". We evaluate nine different decoy designs using public data sets from samples of known composition. Statistically significant performance differen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800792z
更新日期：2009-04-01 00:00:00
abstract：:Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most wide...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500202e
更新日期：2014-08-01 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：:The enormous challenges of mass spectrometry-based metaproteomics are primarily related to the analysis and interpretation of the acquired data. This includes reliable identification of mass spectra and the meaningful integration of taxonomic and functional meta-information from samples containing hundreds of unknown ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501246w
更新日期：2015-03-06 00:00:00
abstract：:Proteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the use of several unintegrated tools. Furthermore, many proteogenomic efforts have be...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400208w
更新日期：2013-06-07 00:00:00
abstract：:The GalNAc O-glycosylation on Ser/Thr residues of extracellular proteins has not been well characterized from a proteomics perspective. We previously reported a sialic acid capture-and-release protocol to enrich tryptic N- and O-glycopeptides from human cerebrospinal fluid glycoproteins using nano-LC-ESI-MS/MS with co...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300963h
更新日期：2013-02-01 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：:Nicotinamide adenine dinucleotide (NAD) is a coenzyme found in all living cells and mediates multiple cellular signaling pathways. In the present study, a 35% decrease of cellular NAD level is achieved by stable expression of the N-terminal truncated CD38, a NAD hydrolase. CD38-expressing (CD38(+)) cells have the lowe...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4010597
更新日期：2014-02-07 00:00:00
abstract：:The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. We have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00445
更新日期：2017-09-01 00:00:00
