Abstract：
:Tropomyosins (Tm) constitute a family of ubiquitous and highly conserved actin-binding proteins, playing essential roles in a variety of biological processes. Tm isoforms produced by multiple Tm encoding genes and alternatively expressed exons along with post-translational modifications (PTMs) regulate Tm function. Therefore, to gain a better understanding of the functional role of Tm, it is essential to fully characterize Tm isoforms. Herein, we developed a top-down high-resolution mass spectrometry (MS)-based targeted proteomics method for comprehensive characterization of Tm isoforms. α-Tm was identified to be the predominant isoform in swine cardiac muscle. We further characterized its sequence and localized the PTMs such as acetylation and phosphorylation as well as amino acid polymorphisms. Interestingly, we discovered a "novel" Tm isoform that does not match with any of the currently available swine Tm sequences. A deep sequencing of this isoform by top-down MS revealed an exact match with mouse β-Tm sequence, suggesting that this "novel" isoform is swine β-Tm which is 100% conserved between swine and mouse. Taken together, we demonstrated that top-down targeted proteomics provides a powerful tool for deep sequencing of Tm isoforms from genetic variations together with complete mapping of the PTM sites.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Peng Y,Chen X,Zhang H,Xu Q,Hacker TA,Ge Ydoi
10.1021/pr301054nsubject
Has Abstractpub_date
2013-01-04 00:00:00pages
187-98issue
1eissn
1535-3893issn
1535-3907journal_volume
12pub_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：:Although tandem mass spectrometry (MS/MS) has become an integral part of proteomics, intensity patterns in MS/MS spectra are rarely weighted heavily in most widely used algorithms because they are not yet fully understood. Here a knowledge mining approach is demonstrated to discover fragmentation intensity patterns an...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070106u
更新日期：2008-01-01 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：:Butyrate, a fermentation product of the large bowel microflora, is potentially protective against the development of colorectal cancer. In vitro, butyrate has been shown to induce apoptosis and inhibit proliferation in numerous cancer cell lines, including colorectal cancer. Although these tumor suppressing properties...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8009929
更新日期：2009-03-01 00:00:00
abstract：:Protein biomarker discovery in the low concentration range of human body fluids requires the enrichment of the proteins of interest. Here we report on a tandem affinity strategy: In the first step, we isolated a human plasma glyco-subproteome of healthy individuals by wheat germ agglutinin (WGA) lectin affinity chroma...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100224y
更新日期：2010-12-03 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：: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：: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 study of protein phosphorylation has grown exponentially in recent years, as it became evident that important cellular functions are regulated by phosphorylation and dephosphorylation of proteins on serine, threonine and tyrosine residues. The use of immobilized metal affinity chromatography (IMAC) to enrich phosp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050224m
更新日期：2005-11-01 00:00:00
abstract：:The purpose of this study was to determine the system-wide consequences of deficiencies in two essential micronutrients, vitamins E and C, on the proteome using zebrafish (Danio rerio) as one of the few vertebrate models that similar to humans cannot synthesize vitamin C. We describe a label-free proteomics workflow t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401108d
更新日期：2014-03-07 00:00:00
abstract：:The ability to distinguish between phosphopeptides of high and low stoichiometry is essential to discover the true extent of protein phosphorylation. We here extend the strategy whereby a peptide sample is briefly split in two identical parts and differentially labeled preceding the phosphatase treatment of one part. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500889v
更新日期：2015-02-06 00:00:00
abstract：:Microbes are known to regulate both gene expression and protein activity through the use of post-translational modifications (PTMs). Common PTMs involved in cellular signaling and gene control include methylations, acetylations, and phosphorylations, whereas oxidations have been implicated as an indicator of stress. S...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070531n
更新日期：2008-02-01 00:00:00
abstract：:Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00278
更新日期：2016-08-05 00:00:00
abstract：:Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and multiple reaction monitoring mass spectrometry (MRM-MS) proteomics analyses were performed on eccrine sweat of healthy controls, and the results were compared with those from individuals diagnosed with schizophrenia (SZ). This is the first large scale study...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2007957
更新日期：2012-04-06 00:00:00
abstract：:Bacillus thuringiensis, a Gram-positive endospore-forming bacterium, is characterized by the formation of parasporal crystals consisting of insecticidal crystal proteins (ICPs) during sporulation. We reveal gene expression profiles and regulatory mechanisms associated with spore and parasporal crystal formation based ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4003728
更新日期：2013-12-06 00:00:00
abstract：:Glycans play major roles in living organisms. Thus, essential information is required on diverse glycans, their location, and moieties in proteins, as well as for technology in a high-throughput manner, for improving functional glycomics. In the present study, we describe a new approach involving a 2-D array, which ha...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070392+
更新日期：2008-03-01 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：:Glioblastoma (GBM) is the most common adult primary brain tumor. Despite aggressive multimodal therapy, the survival of patients with GBM remains dismal. However, recent evidence has demonstrated the promise of bone marrow-derived mesenchymal stem cells (BM-hMSCs) as a therapeutic delivery vehicle for anti-glioma agen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00076
更新日期：2015-06-05 00:00:00
abstract：:A major challenge in developing cell therapies is reliable characterization of the cell product at the molecular level. Fresh autologous and passaged human bone marrow enriched for stem and mesenchymal stromal stem cells have been used to regenerate bone. We report the proteome of an innovative autologous human bone m...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr801064u
更新日期：2009-04-01 00:00:00
abstract：:A robust method has been developed that allows analysis of both N- and O-linked oligosaccharides released from glycoproteins separated using 2D-PAGE and then electroblotted to PVDF membrane. This analysis provides efficient oligosaccharide profiling applicable to glycoproteomic analysis. The method involves the enzyma...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr025538d
更新日期：2002-11-01 00:00:00
abstract：:Many neurodegenerative diseases, such as Parkinson's disease, can be directly correlated with the deregulation in neuronal signaling. Hence, it is indispensable for therapy development to understand the participating signaling processes. Because the activity of the involved protein kinases is of major interest for the...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500163r
更新日期：2014-08-01 00:00:00
abstract：:The ThinPrep cervical smear is widely used in clinical practice for the cytological and molecular screening against abnormal cells and Human Papillomavirus (HPV) infection. Current advancements made to LC-MS proteomics include the use of stable isotope labeling for the in-depth analysis of proteins in complex clinical...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301067r
更新日期：2013-05-03 00:00:00
abstract：:Coronary artery disease is one of the most frequent causes of morbidity and mortality worldwide. It is even more prevalent in patients with type 2 diabetes mellitus who suffer from obesity and increased accumulation of epicardial fat with a possible contributing role in the development of coronary artery disease. We p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00269
更新日期：2020-10-02 00:00:00
abstract：:Metabolic phenotyping of tissues uses metabolomics and lipidomics to measure the relative polar and nonpolar (lipid) metabolite levels in biological samples. This approach aims to understand disease biochemistry and identify biochemical markers of disease. Sample preparation methods must be reproducible, sensitive (hi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00660
更新日期：2021-01-01 00:00:00
abstract：:Protein-protein interactions play a major role in the molecular machinery of life, and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hier...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00066
更新日期：2020-07-02 00:00:00
abstract：:High-throughput technologies, such as proteomic screening and DNA micro-arrays, produce vast amounts of data requiring comprehensive analytical methods to decipher the biologically relevant results. One approach would be to manually search the biomedical literature; however, this would be an arduous task. We developed...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0340227
更新日期：2003-07-01 00:00:00
abstract：:In line with the aims of the Chromosome-based Human Proteome Project and the Biology/Disease-based Human Proteome Project, we have been studying differentially expressed transcripts and proteins in gliomas—the most prevalent primary brain tumors. Here, we present a perspective on important insights from this analysis ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00488
更新日期：2015-09-04 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：:Irritable Bowel Syndrome (IBS) is a common multifactorial intestinal disorder for which the aetiology remains largely undefined. Here, we have used a Trichinella spiralis (T. spiralis)-induced model of post-infective IBS, and the effects of probiotic bacteria on gut dysfunction have been investigated using a metabonom...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060157b
更新日期：2006-09-01 00:00:00
abstract：:An alternative sieving matrix, replaceable cross-linked polyacrylamide (rCPA), was developed for sodium dodecyl sulfate capillary gel electrophoresis (SDS-CGE) separation of proteins. This rCPA could be conveniently pressurized into separation capillaries under a pressure of 80 psi. SDS-CGE separations using this matr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0500206
更新日期：2005-05-01 00:00:00
