Abstract：
:Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MS(n)). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95% correct MS(2) assignments from known synthetic data, > 98% agreement with an established MS(2) assignment algorithm (Ascore), and >92% agreement with visual inspection of MS(3) and MS(4) spectra.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Ruttenberg BE,Pisitkun T,Knepper MA,Hoffert JDdoi
10.1021/pr800169ksubject
Has Abstractpub_date
2008-07-01 00:00:00pages
3054-9issue
7eissn
1535-3893issn
1535-3907journal_volume
7pub_type
杂志文章abstract：:Many proteins possess intrinsic disorder (ID) and lack a rigid three-dimensional structure in at least part of their sequence. ID has been hypothesized to influence protein-protein and protein-ligand interactions. We calculated ID for nearly 400 vertebrate and invertebrate members of the biomedically important nuclear...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8003024
更新日期：2008-10-01 00:00:00
abstract：:Pancreatic cancer is a devastating disease and early diagnosis and treatment are essential to improve the prognosis. We previously showed that α-fibrinogen containing hydroxylated proline residues at positions 530 and 565 is increased in plasma of pancreatic cancer patients. However, no antibody specific for hydroxyla...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3008144
更新日期：2013-02-01 00:00:00
abstract：:We aimed to determine the time-course of metabolic changes related to the early onset of insulin resistance (IR), trying to evidence breaking points preceding the appearance of the clinical IR phenotype. The model chosen was the fructose (FRU)-fed rat compared to controls fed with starch. We focused on the hepatic met...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00043
更新日期：2016-06-03 00:00:00
abstract：:Sexual dimorphism is initialed by the components of the sex determination pathway and is most evident in gonads and germ cells. Although striking dimorphic expressions have been detected at the transcriptional level between the silkworm larval testis and the ovary, the sex-dimorphic expressions at the protein level ha...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300920z
更新日期：2013-06-07 00:00:00
abstract：:Protein or peptide sample losses could accompany all steps of the proteomic analysis workflow. We focused on suppression of sample adsorptive losses during sample storage in autosampler vials. We examined suppression capabilities of six different sample injection solutions and seven types of autosampler vial surfaces ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400183v
更新日期：2013-06-07 00:00:00
abstract：:We recently developed a novel method for analysis of collagen O-glycosylations, which include galactosyl-hydroxylysine (GHL) and glucosyl-galactosyl-hydroxylysine (GGHL), using hydrazide chemistry (Taga, Y., Mol. Cell. Proteomics 2012, 11 (6), M111.010397). Here we investigated an overglycosylation model of collagen p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400079d
更新日期：2013-05-03 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：:Accurate and sensitive detection of protein-protein and protein-RNA interactions is key to understanding their biological functions. Traditional methods to identify these interactions require cell lysis and biochemical manipulations that exclude cellular compartments that cannot be solubilized under mild conditions. H...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500196b
更新日期：2014-12-05 00:00:00
abstract：:While the proteome defines the expressed gene products, the metabolome results from reactions controlled by such gene products. Plasma represents an accessible "window" to the metabolome both in regard of availability and content. The wide range of the plasma metabolome, in terms of molecular diversity and abundance, ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8001639
更新日期：2008-08-01 00:00:00
abstract：:The bacterial ribosomal protein S12 contains a universally conserved D88 residue on a loop region thought to be critically involved in translation due to its proximal location to the A site of the 30S subunit. While D88 mutants are lethal this residue has been found to be post-translationally modified to β-methylthioa...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3009435
更新日期：2013-03-01 00:00:00
abstract：:Hydrogen peroxide (H(2)O(2)) and nitric oxide ((•)NO) elicit numerous processes in plants. However, our knowledge of H(2)O(2) and (•)NO-responsive proteins is limited. The present study aimed to identify proteins whose accumulation levels were regulated by these signaling molecules in citrus leaves. To address this qu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100782h
更新日期：2010-11-05 00:00:00
abstract：:Proteins and peptides present within clinical samples represent a valuable library of information regarding the ongoing processes within cells and tissues in health and disease. We have developed and validated novel technology applications that can be used to characterize the patterns of global protein expression in t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050122w
更新日期：2005-07-01 00:00:00
abstract：:Reported in this work are the development of mass spectrometric immunoassay (MSIA) devices and methods for the qualitative analysis of IGF-1 and -2, and the rigorous quantification of IGF-1 from human plasma. A method involving addition of SDS in moderate concentration to unfractionated plasma for disrupting IGF/IGFBP...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0499388
更新日期：2004-07-01 00:00:00
abstract：:Dipetalogaster maxima is a blood-sucking Hemiptera that inhabits sylvatic areas in Mexico. It usually takes its blood meal from lizards, but following human population growth, it invaded suburban areas, feeding also on humans and domestic animals. Hematophagous insect salivary glands produce potent pharmacologic compo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100866h
更新日期：2011-02-04 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：:Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-thr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7008252
更新日期：2008-04-01 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：: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：:The development of medical interventions for the preservation of disease-free longevity would be facilitated by markers that predict healthy aging. Altered protein N-glycosylation patterns have been found with increasing age and several disease states. Here we investigate whether glycans derived from the total glycopr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1009959
更新日期：2011-04-01 00:00:00
abstract：:To cope with sudden changes in the external environment, the budding yeast Saccharomyces cerevisiae orchestrates a multifaceted response that spans many levels of physiology. Several studies have interrogated the transcriptome response to endoplasmic reticulum (ER) stress and the role of regulators such as the Ire1 ki...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00253
更新日期：2020-08-07 00:00:00
abstract：:Fulminant type 1 diabetes (FT1DM) is a relatively new clinical entity featured by acute destruction of pancreatic beta cells. Clinical consequences of FT1DM could be fatal when timely medications are not provided, suggesting the particular importance of rapid and accurate diagnosis. Here we report a serum metabonomics...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300523x
更新日期：2012-09-07 00:00:00
abstract：:The HIV-1-associated neurocognitive disorder occurs in approximately one-third of infected individuals. It has persisted in the current era of antiretroviral therapy, and its study is complicated by the lack of biomarkers for this condition. Since the cerebrospinal fluid is the most proximal biofluid to the site of pa...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800854t
更新日期：2009-05-01 00:00:00
abstract：:POPX2 is a serine/threonine phosphatase belonging to the protein phosphatase 2C (PP2C) family that has been found to be elevated in invasive breast cancer cells. Silencing of POPX2 results in lower cell motility and invasiveness. The molecular mechanism of POPX2-regulated cell motility is not well understood. To ident...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301113c
更新日期：2013-06-07 00:00:00
abstract：:We analyzed the whole-cell protein content of gastrocnemius muscles from rats in different thyroid states. Twenty differentially expressed proteins were unambiguously identified. They were involved in substrates and energy metabolism, stress response, cell structure, and gene expression. This study represents the firs...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0701299
更新日期：2007-08-01 00:00:00
abstract：:Traditional measures of short-term stress response such as fecal glucocorticoid metabolites (FGM) are widely used in controlled settings to quantify the intensity of stimulation to which cattle are exposed. However, FGMs present several methodological and interpretation pitfalls when applied on animals in free-ranging...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00655
更新日期：2020-02-07 00:00:00
abstract：:The process of extracting comprehensive proteome representations is a crucial step for many proteomic studies. While antibody microarrays are an evolving and promising methodology in proteomics, the issue of protein extraction from tissues for this kind of analysis has never been addressed. Here, we describe a single-...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900844q
更新日期：2010-02-05 00:00:00
abstract：:Starting in 2007, we have grown soybean (Glycine max [L.] Merr. variety Soniachna) and flax (Linum usitatissimum, L. variety Kyivskyi) in the radio-contaminated Chernobyl area and analyzed the seed proteomes. In the second-generation flax seeds, we detected a 12% increase in oil content. To characterize the bases for ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400528m
更新日期：2013-11-01 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：:Shotgun proteomics produces collections of tandem mass spectra that contain all the data needed to identify mutated peptides from clinical samples. Identifying these sequence variations, however, has not been feasible with conventional database search strategies, which require exact matches between observed and expect...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900850m
更新日期：2010-04-05 00:00:00
abstract：:Our cyanylation (CN)-based methodology for determining disulfide structure of cystinyl proteins overcomes the limitations of conventional proteolytic methods. However, the CN-based method has the potential drawback that occasionally some CN-induced cleavage fragments may not be detected. We show that CN-based methods ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049961t
更新日期：2004-07-01 00:00:00
