Abstract：
:There are three quantitative phosphoproteomic strategies most commonly used to study receptor tyrosine kinase (RTK) signaling. These strategies quantify changes in: (1) all three forms of phosphosites (phosphoserine, phosphothreonine and phosphotyrosine) following enrichment of phosphopeptides by titanium dioxide or immobilized metal affinity chromatography; (2) phosphotyrosine sites following anti- phosphotyrosine antibody enrichment of phosphotyrosine peptides; or (3) phosphotyrosine proteins and their binding partners following anti-phosphotyrosine protein immunoprecipitation. However, it is not clear from literature which strategy is more effective. In this study, we assessed the utility of these three phosphoproteomic strategies in RTK signaling studies by using EphB receptor signaling as an example. We used all three strategies with stable isotope labeling with amino acids in cell culture (SILAC) to compare changes in phosphoproteomes upon EphB receptor activation. We used bioinformatic analysis to compare results from the three analyses. Our results show that the three strategies provide complementary information about RTK pathways.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Zhang G,Neubert TAdoi
10.1021/pr200697xsubject
Has Abstractpub_date
2011-12-02 00:00:00pages
5454-62issue
12eissn
1535-3893issn
1535-3907journal_volume
10pub_type
杂志文章abstract：:In the framework of the C-HPP, our Franco-Swiss consortium has adopted chromosomes 2 and 14, coding for a total of 382 missing proteins (proteins for which evidence is lacking at protein level). Over the last 4 years, the French proteomics infrastructure has collected high-quality data sets from 40 human samples, incl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5010345
更新日期：2015-09-04 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200088w
更新日期：2011-06-03 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300123g
更新日期：2012-08-03 00:00:00
abstract：:Gas chromatography-mass spectrometry (GC-MS) platforms are typically run in electron ionization (EI) mode for mass spectral matching and metabolite annotation. With the advent of high resolution mass spectrometry (HRMS), soft ionization techniques such as chemical ionization (CI) may provide additional coverage for co...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00774
更新日期：2020-07-02 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：:Renal cell carcinoma (RCC) tissue is composed of a mixture of neoplastic and normal cells, which complicate proteome analysis. The aim of our study was to investigate whether it is feasible to establish primary cell cultures of RCC and of renal cortex maintaining the tissue phenotype along with a more homogeneous and ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050002o
更新日期：2005-09-01 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：:Pancreatic cystic neoplasms represent 10-15% of primary cystic masses of the pancreas. While pancreatic cysts are detected with an increasing frequency due to the use of advanced imaging modalities in clinical practice, the diagnosis of pancreatic cystic neoplasms remains unsatisfactory because available diagnostic te...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2000557
更新日期：2011-05-06 00:00:00
abstract：:The current technique used for microbial identification in hospitals is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, it suffers from important limitations, in particular, for closely related species or when the database used for the identification lacks the appr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00351
更新日期：2021-01-01 00:00:00
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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
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00918
更新日期：2017-05-05 00:00:00
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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：:We have expanded our recent on-line LC-MS platform for large peptide analysis to combine collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced (CRCID) species derived from ETD to determine sites of phosphorylation and glycosylation modifications, as well as t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070313u
更新日期：2007-11-01 00:00:00
abstract：:HER2-testing in breast and gastric cancers is mandatory for the treatment with trastuzumab. We hypothesized that imaging mass spectrometry (IMS) of breast cancers may be useful for generating a classifier that may determine HER2-status in other cancer entities irrespective of primary tumor site. A total of 107 breast ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100573s
更新日期：2010-12-03 00:00:00
abstract：:Isobaric tagging is the method of choice in mass-spectrometry-based proteomics for comparing several conditions at a time. Despite its multiplexing capabilities, some drawbacks appear when multiple experiments are merged for comparison in large sample-size studies due to the presence of missing values, which result fr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00110
更新日期：2018-06-01 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
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00654
更新日期：2016-12-02 00:00:00
abstract：:The mechanisms whereby Mycobacterium tuberculosis (Mtb) rewires the host metabolism in vivo are surprisingly unexplored. Here, we used three high-resolution mass spectrometry platforms to track altered lung metabolic changes associated with Mtb infection of mice. The multiplatform data sets were merged using consensus...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00868
更新日期：2020-05-01 00:00:00
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, ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00756
更新日期：2015-12-04 00:00:00
abstract：:Analysis of the cerebrospinal fluid (CSF) proteome has proven valuable to the study of neurodegenerative disorders. To identify new protein/pathway alterations and candidate biomarkers for amyotrophic lateral sclerosis (ALS), we performed comparative proteomic profiling of CSF from sporadic ALS (sALS), healthy control...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00804
更新日期：2015-11-06 00:00:00
abstract：:The role played by the degree of folding of protein backbones in explaining the binding energetics of protein-ligand interactions has been studied. We analyzed the protein/peptide interactions in the RNase-S system in which amino acids at two positions of the peptide S have been mutated. The global degree of folding o...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0503174
更新日期：2006-01-01 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：:Phosphorylation enhances IGFBP-1 binding to IGF-I, thereby limiting the bioavailability of IGF-I that may be important in fetal growth. Our goal in this study was to determine whether changes in site-specific IGFBP-1 phosphorylation were unique to fetal growth restriction. To establish a link, we compared IGFBP-1 phos...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900987n
更新日期：2010-04-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4005025
更新日期：2013-09-06 00:00:00
abstract：:A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00474
更新日期：2015-09-04 00:00:00
abstract：:Protein tyrosine nitration by oxidative and nitrate stress is important in the pathogenesis of many inflammatory or aging-related diseases. Mass spectrometry analysis of protein nitrotyrosine is very challenging because the non-nitrated peptides suppress the signals of the low-abundance nitrotyrosine (NT) peptides. No...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00275
更新日期：2017-08-04 00:00:00
abstract：:The current report describes the use of CapLC-ESI-Q/TOF-MS for investigating the proteome profiles of hypertonic saline-induced sputum samples from 56 smokers. The severity of their lung disease ranged from normal (healthy smokers) to chronic bronchitis, chronic obstructive pulmonary disease (COPD), and COPD with emph...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070440q
更新日期：2007-12-01 00:00:00
abstract：:Knowledge of protein subcellular localization assists in the elucidation of protein function and understanding of different biological mechanisms that occur at discrete subcellular niches. Organelle-centric proteomics enables localization of thousands of proteins simultaneously. Although such techniques have successfu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4008464
更新日期：2014-02-07 00:00:00
abstract：:Visual signal transduction takes place on the surface of flat membrane vesicles called photoreceptor discs, which reside inside the light-sensitive outer segment organelle of vertebrate photoreceptor cells. Although biochemical studies have indicated that discs are built with a handful of highly specialized proteins, ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4003678
更新日期：2013-06-07 00:00:00
abstract：:Advances in high-throughput proteomics have led to a rapid increase in the number, size, and complexity of the associated data sets. Managing and extracting reliable information from such large series of data sets require the use of dedicated software organized in a consistent pipeline to reduce, validate, exploit, an...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00853
更新日期：2016-10-07 00:00:00
