Abstract：
:A comprehensive glycan map was constructed for the top eight abundant glycoproteins in plasma using both specific and nonspecific enzyme digestions followed by nano liquid chromatography (LC)-chip/quadrupole time-of-flight mass spectrometry (MS) analysis. Glycopeptides were identified using an in-house software tool, GPFinder. A sensitive and reproducible multiple reaction monitoring (MRM) technique on a triple quadrupole MS was developed and applied to quantify immunoglobulins G, A, M, and their site-specific glycans simultaneously and directly from human serum/plasma without protein enrichments. A total of 64 glycopeptides and 15 peptides were monitored for IgG, IgA, and IgM in a 20 min ultra high performance (UP)LC gradient. The absolute protein contents were quantified using peptide calibration curves. The glycopeptide ion abundances were normalized to the respective protein abundances to separate protein glycosylation from protein expression. This technique yields higher method reproducibility and less sample loss when compared with the quantitation method that involves protein enrichments. The absolute protein quantitation has a wide linear range (3-4 orders of magnitude) and low limit of quantitation (femtomole level). This rapid and robust quantitation technique, which provides quantitative information for both proteins and glycosylation, will further facilitate disease biomarker discoveries.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Hong Q,Ruhaak LR,Stroble C,Parker E,Huang J,Maverakis E,Lebrilla CBdoi
10.1021/acs.jproteome.5b00756subject
Has Abstractpub_date
2015-12-04 00:00:00pages
5179-92issue
12eissn
1535-3893issn
1535-3907journal_volume
14pub_type
杂志文章abstract：:Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively exp...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr060623x
更新日期：2007-02-01 00:00:00
abstract：:Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results....
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00113
更新日期：2019-01-04 00:00:00
abstract：:Molecular imaging of tissue by MALDI mass spectrometry is a powerful tool for visualizing the spatial distribution of constituent analytes with high molecular specificity. Although the technique is relatively young, it has already contributed to the understanding of many diverse areas of human health. In recent years,...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr060346u
更新日期：2006-11-01 00:00:00
abstract：:Recently, we reported comparative analysis of glycoproteins which express cancer-specific N-glycans on various cancer cells and identified 24 glycoproteins having polylactosamine (polyLacNAc)-type N-glycans that are abundantly present in malignant cells [ Mitsui et al., J. Pharm. Biomed. Anal. 2012 , 70 , 718 - 726 ]....
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401015b
更新日期：2014-02-07 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：:Gene-encoded antimicrobial peptides (AMPs) kill bacteria very efficiently by either lytic mechanisms or inhibition of specific bacterial targets. Proline-rich AMPs (PrAMPs), for example, produced in insects and mammals rely on the second mechanism. They bind to the 70 kDa bacterial heat shock protein DnaK and the 60 k...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00283
更新日期：2015-08-07 00:00:00
abstract：:MSI is a molecular imaging technique that allows for the generation of topographic 2D maps for various endogenous and some exogenous molecules without prior specification of the molecule. In this paper, we start with the premise that a region of interest (ROI) is given to us based on preselected morphological criteria...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101159e
更新日期：2011-04-01 00:00:00
abstract：:Quorum sensing (QS) in Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of bacterial leaf streak, is mediated by the diffusible signal factor (DSF). DSF-mediating QS has been shown to control virulence and a set of virulence-related functions; however, the expression profiles and functions of extracellular pro...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4001543
更新日期：2013-07-05 00:00:00
abstract：:Reversible phosphorylations play a critical role in most biological pathways. Hence, in signaling studies great effort has been put into identification of a maximum number of phosphosites per experiment. Mass spectrometry (MS)-based phosphoproteomics approaches have been proven to be an ideal analytical method for map...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200092z
更新日期：2011-08-05 00:00:00
abstract：:The development of the nematode Caenorhabditis elegans is a highly dynamic process. Although various studies have assessed global transcriptome changes, information on the dynamics of the proteome during ontogenesis is not available. We metabolically labeled C. elegans by using ¹⁵N ammonium chloride as a precursor in ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300385v
更新日期：2012-09-07 00:00:00
abstract：:"Omics" studies reported to date have dealt with either thoroughly characterized single species or poorly explored meta-microbial communities. However, these techniques are capable of producing highly informative data for the analysis of interactions between two organisms. We examined the bacterial interaction between...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100989c
更新日期：2011-02-04 00:00:00
abstract：:Recoding refers to the reprogramming of mRNA translation by nonstandard read-out rules. In this study, we used stable isotope labeling with amino acids in cell culture (SILAC) technology to investigate the proteome of host-adapted Salmonella serovars, which are characteristic of accumulation of pseudogenes. Interestin...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200904c
更新日期：2012-03-02 00:00:00
abstract：:A metabonomic study was performed to investigate the biochemical perturbation of the serum samples from liver failure patients induced by hepatitis B virus (HBV; n=24) and control normal subjects (n=23). The serum metabonome was detected using gas chromatography-mass spectrometry (GC-MS) technique integrated with a co...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060591d
更新日期：2007-07-01 00:00:00
abstract：:During the development of cancer, changes in cellular glycosylation are observed, indicating that alterations of the glycome occur in extracellular fluids as well as in serum and could therefore serve as tumor biomarkers. In the case of epithelial ovarian cancer (EOC), common tumor markers such as CA125 are known to h...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400405x
更新日期：2013-09-06 00:00:00
abstract：:Francisella tularensis is a Gram-negative bacterium that causes the zoonotic disease tularemia. The historical development of tularemia as a biological weapon has led to it being characterized by the CDC as a category A biothreat agent. Neither posttranslational modification (PTM) of proteins, in particular lysine ace...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00512
更新日期：2020-04-03 00:00:00
abstract：:As central tissue of glucose homeostasis, islet has been an important focus of diabetes research. Phosphorylation plays pivotal roles in islet function, especially in islet glucose-stimulated insulin secretion. A systematic view on how phosphorylation networks were coordinately regulated in this process remains lackin...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00507
更新日期：2015-11-06 00:00:00
abstract：:Although the "missing protein" is a temporary concept in C-HPP, the biological information for their "missing" could be an important clue in evolutionary studies. Here we classified missing-protein-encoding genes into two groups, the genes encoding PE2 proteins (with transcript evidence) and the genes encoding PE3/4 p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00450
更新日期：2015-12-04 00:00:00
abstract：:We report a hybrid search method combining database and spectral library searches that allows for a straightforward approach to characterizing the error rates from the combined data. Using these methods, we demonstrate significantly increased sensitivity and specificity in matching peptides to tandem mass spectra. The...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101130b
更新日期：2011-05-06 00:00:00
abstract：:Ralstonia eutropha H16 is a denitrifying microorganism able to use nitrate and nitrite as terminal electron acceptors under oxygen deprivation. To identify proteins showing an altered expression pattern in response to oxygen supply, R. eutropha cells grown aerobically and anaerobically were compared in a comprehensive...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500491r
更新日期：2014-10-03 00:00:00
abstract：:An unusual sulfotyrosine-, phosphoserine-containing motif was mapped on a differentially post-translationally modified 60 residue antimicrobial neuroendocrine peptide called chrombacin. The study was performed by high resolution FT MS using complementary fragmentation techniques. The peptide was analyzed at low levels...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7006686
更新日期：2008-02-01 00:00:00
abstract：:Yeast two-hybridization (Y2H) is a classical method to study protein-protein interactions in organisms, and the top limitation of Y2H is the high ratio of false negatives and false positives. The most efficient way to reduce this error is to improve the quality of the library. The traditional library quality evaluatio...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00189
更新日期：2020-08-07 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：:Protein biomarkers are critical for diagnosis, prognosis, and treatment of disease. The transition from protein biomarker discovery to verification can be a rate limiting step in clinical development of new diagnostics. Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) is becoming an imp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2006704
更新日期：2012-02-03 00:00:00
abstract：:The secreted proteins of bacteria are usually accompanied by virulence factors, which can cause inflammation and damage host cells. Identifying the secretomes arising from the interactions of bacteria and host cells could therefore increase understanding of the mechanisms during initial pathogenesis. The present study...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00584
更新日期：2017-01-06 00:00:00
abstract：:The gene transfer agent of Rhodobacter capsulatus (GTA) is a unique phage-like particle that exchanges genetic information between members of this same species of bacterium. Besides being an excellent tool for genetic mapping, the GTA has a number of advantages for biotechnological and nanoengineering purposes. To fac...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8006045
更新日期：2009-02-01 00:00:00
abstract：:Temperature is one of the most critical parameters for yeast growth, and it has deep consequences in many industrial processes where yeast is involved. Nevertheless, the metabolic changes required to accommodate yeast cells at high or low temperatures are still poorly understood. In this work, the ultimate responses o...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00921
更新日期：2018-06-01 00:00:00
abstract：:A biphasic monolithic capillary column with 10 cm segment of strong-cation exchange monolith and 65 cm segment of reversed-phase monolith was prepared within a single 100 microm i.d. capillary. Separation performance of this column was evaluated by a five-cycle online multidimensional separation of 10 microg tryptic d...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr700562b
更新日期：2008-01-01 00:00:00
abstract：: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 spec...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00045
更新日期：2019-04-05 00:00:00
abstract：:Over the past few years, awareness has risen that for mass-spectrometry-based proteomics methods to mature into everyday analytical and clinical practices, extensive quality assessment is mandatory. A currently overlooked source of qualitative information originates from the mass spectrometer itself. Apart from the ac...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00127
更新日期：2015-05-01 00:00:00
abstract：:We have studied the role(s) of maturation drying in the acquisition of germinability, seedling vigor and pathogen resistance by comparing the proteome changes in maize embryo and endosperm during mature and prematurely imposed drying. Prematurely imposed dried seeds at 40 days after pollination (DAP) germinated almost...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4007574
更新日期：2014-02-07 00:00:00
