Abstract：
:Proteomics methods are being increasingly used to study archaeological and palaeontological bone, assisting in species identification and phylogenetic studies as well as improving our understanding of bone diagenesis. More recently, there are developing interests in the study of post-translational modifications, some of which are potentially diagnostic of decay, but none of the previous extraction methods have been developed in light of this. To be able to record close to natural deamidation levels of samples, an extraction procedure should minimize laboratory-induced decay, such as asparagine and glutamine deamidations, which are considered most strongly related with decay and known to occur frequently with standard laboratory procedures. Here we tested numerous methods to identify an optimal approach of extracting proteins from bone while minimizing artificial decay. Using a weak acid to partially demineralize the bone sample, then subsequent incubation of the acid insoluble fraction with guanidine hydrochloride and enzymatic digestion in ammonium acetate, we observed an ∼50% reduction in deamidation while also substantially decreasing the protocol length. We propose this optimized method as appropriate for studies of archaeological, palaeontological, as well as potentially forensic investigations using proteomics where decay measurements could act as "molecular timers".
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Procopio N,Buckley Mdoi
10.1021/acs.jproteome.6b00564subject
Has Abstractpub_date
2017-02-03 00:00:00pages
447-458issue
2eissn
1535-3893issn
1535-3907journal_volume
16pub_type
杂志文章abstract：:Expansion of human articular chondrocytes (HACs) in serum-free medium (SFM) has been shown to be enhanced by the control of medium osmolality. HACs attained better growth when cultured at osmolalities lower than the average osmolality found in articular cartilage in vivo, although the specific causes for this improved...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100136q
更新日期：2010-05-07 00:00:00
abstract：:When analyzing proteins in complex samples using tandem mass spectrometry of peptides generated by proteolysis, the inference of proteins can be ambiguous, even with well-validated peptides. Unresolved questions include whether to show all possible proteins vs a minimal list, what to do when proteins are inferred ambi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200039p
更新日期：2011-07-01 00:00:00
abstract：:Phytopathogenic fungi are one of the most damaging plant parasitic organisms, and can cause serious diseases and important yield losses in crops. The study of the biology of these microorganisms and the interaction with their hosts has experienced great advances in recent years due to the development of moderm, holist...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr200873p
更新日期：2012-01-01 00:00:00
abstract：:Campylobacter jejuni is the most common cause of bacterial gastroenteritis in the developed world. Immunoproteomics highlighted a 42-45 kDa antigen that comigrated on two-dimensional (2-DE) gels with the C. jejuni major outer membrane protein (MOMP). Predictive analysis revealed two candidates for the identity of the ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900544x
更新日期：2009-10-01 00:00:00
abstract：:Dehydroeffusol (DHE) is a phenanthrene isolated from the Chinese medicinal plant Juncus effusus. Biological evaluation of DHE reveals in vitro and in vivo anticancer effects. We performed a shotgun proteomic analysis using liquid chromatography-tandem mass spectrometry to investigate the changes in the protein profile...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00227
更新日期：2018-07-06 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：:We analyzed a unique rice (Oryza sativa L.) blast lesion mimic (blm) mutant for differentially expressed proteins in leaves of one- and two-week-old seedlings manifesting the lesion mimic phenotype. Gel-based one- and two-dimensional electrophoresis (1- and 2-DGE) was performed using leaves (blm and wild-type, WT) bef...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060092c
更新日期：2006-10-01 00:00:00
abstract：:Fast (120 s) and high-throughput (more than six samples at once) in-gel trypsin digestion of proteins using sonoreactor technology has been achieved. Successful protein identification was done by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF-MS. Specific identification of the ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060508m
更新日期：2007-02-01 00:00:00
abstract：:Approximately 25% of eukaryotic proteins possessing homology to at least two transmembrane domains are predicted to be embedded in biological membranes. Nevertheless, this group of proteins is not usually well represented in proteome-wide experiments due to their refractory nature. Here we present a quantitative mass ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200759m
更新日期：2012-02-03 00:00:00
abstract：:As a result of the complexity and dynamic range of the cellular proteome, including mutual interactions and interactions with other molecules, focused proteomic approaches are important to study subsets of physiologically important proteins. In one such approach, a small molecule or part of a protein is immobilized on...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060278b
更新日期：2006-09-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00822
更新日期：2021-01-04 00:00:00
abstract：:Chronic kidney disease (CKD) has emerged as a major public health problem worldwide. It frequently progresses to end-stage renal disease, which is related to very high cost and mortality. Novel biomarkers can provide insight into the novel mechanism, facilitate early detection, and monitor progression of CKD and its r...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00583
更新日期：2016-10-07 00:00:00
abstract：:Quantitative proteomics experiments, using for instance isobaric tandem mass tagging approaches, are conducive to measuring changes in protein abundance over multiple time points in response to one or more conditions or stimulations. The aim is often to determine which proteins exhibit similar patterns within and acro...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00615
更新日期：2019-02-01 00:00:00
abstract：:Facing the explosion of newly generated protein sequences in the post genomic era, we are challenged to develop an automated method for fast and reliably annotating their subcellular locations. Knowledge of subcellular locations of proteins can provide useful hints for revealing their functions and understanding how t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060167c
更新日期：2006-08-01 00:00:00
abstract：:Diosgenin (DIO), the starting material for the synthesis of steroidal anti-inflammatory drugs in the pharmaceutical industry, has been previously demonstrated to display pharmaceutical effects against cerebral ischemic reperfusion (I/R). However, the alterations of brain proteome profiles underlying this treatment rem...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00667
更新日期：2020-03-06 00:00:00
abstract：:Aberrant protein phosphorylation plays important roles in cancer-related cell signaling. With the goal of achieving multiplexed, comprehensive, and fully automated relative quantitation of site-specific phosphorylation, we present a simple label-free strategy combining an automated pH/acid-controlled IMAC procedure an...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100394u
更新日期：2010-11-05 00:00:00
abstract：:The development of computational strategies for the quantitative characterization of the functional mechanisms of SARS-CoV-2 spike proteins is of paramount importance in efforts to accelerate the discovery of novel therapeutic agents and vaccines combating the COVID-19 pandemic. Structural and biophysical studies have...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00654
更新日期：2020-11-06 00:00:00
abstract：:The neurodegenerative disorder Alzheimer's disease (AD) is the most common cause of dementia in the elderly. The presence of neurofibrillary tangles, consisting of hyperphosphorylated tau protein, is one of the major neuropathologic characteristics of the disease, making this protein an attractive biomarker for AD and...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7008669
更新日期：2008-05-01 00:00:00
abstract：:Proteomics has been applied to study intracellular bacteria and phagocytic vacuoles in different host cell lines, especially macrophages (Mφs). For mycobacterial phagosomes, few studies have identified over several hundred proteins for systems assessment of the phagosome maturation and antigen presentation pathways. M...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101245u
更新日期：2011-05-06 00:00:00
abstract：:Monoassociation of germfree Interleukin 10 gene deficient (IL-10-/-) 129SvEv but not wild-type mice with Enterococcus faecalis induces severe chronic colitis. Bacterial strain-specific effects on the development of chronic intestinal inflammation are not understood. We investigated the molecular mechanisms of E. faeca...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800785m
更新日期：2009-03-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101218d
更新日期：2011-05-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8010028
更新日期：2009-08-01 00:00:00
abstract：:Ricin is a type II ribosome-inactivating protein toxin consisting of A and B chains linked by one interchain disulfide bond. Because of its high toxicity depending on both chains together, confirming the presence of both A and B chains of intact ricin is required during the investigation of the illegal production and ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00458
更新日期：2021-01-01 00:00:00
abstract：:Various biological activities of immunoglobulin G (IgG) including antibody-dependent cellular cytotoxicity (ADCC) are modulated by the structural features of the N-glycans in the Fc part. In this study, we describe a population of IgG1 alloantibodies which are formed during pregnancy against human platelet antigens (H...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800651j
更新日期：2009-02-01 00:00:00
abstract：:The notion of a gamete recognition system that alerts females to the presence of gametes in their reproductive tract profoundly influences our understanding of the physiology of events leading to conception and the bearing of offspring. Here, we show that the female responds to gametes within her tract by modulating t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070349m
更新日期：2007-12-01 00:00:00
abstract：:Populus tremula L. x P. alba L. (Populus x canescens (Aiton) Smith), clone INRA 717-1-B4, saplings were subjected to 120 ppb ozone exposure for 28 days. Chloroplasts were isolated, and the membrane proteins, solubilized using the detergent 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), were analyzed in a differen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1012009
更新日期：2011-07-01 00:00:00
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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：: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：:In this review, we lead the reader through the evolution of proteomics application to the study of quality control in production processes of foods (including food of plant origin and transgenic plants in particular, but also meat, wine and beer, and milk) and food safety (screening for foodborne pathogens). These top...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr2008829
更新日期：2012-01-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300878y
更新日期：2013-02-01 00:00:00
