Abstract:
:Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m (3) of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. To identify key proteins related to tree growth, productivity and responses to environmental factors, a proteomic approach is being utilized. In this paper, we present the first report of the 2-DE protein reference map of physiologically mature P. radiata needles, as a basis for subsequent differential expression proteomic studies related to growth, development, biomass production and responses to stresses. After TCA/acetone protein extraction of needle tissue, 549 +/- 21 well-resolved spots were detected in Coommassie-stained gels within the 5-8 pH and 10-100 kDa M(r) ranges. The analytical and biological variance determined for 450 spots were of 31 and 42%, respectively. After LC/MS/MS analysis of in-gel tryptic digested spots, proteins were identified by using the novel Paragon algorithm that tolerates amino acid substitution in the first-pass search. It allowed the confident identification of 115 out of the 150 protein spots subjected to MS, quite unusual high percentage for a poor sequence database, as is the case of P. radiata. Proteins were classified into 12 or 18 groups based on their corresponding cell component or biological process/pathway categories, respectively. Carbohydrate metabolism and photosynthetic enzymes predominate in the 2-DE protein profile of P. radiata needles.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Valledor L,Castillejo MA,Lenz C,Rodríguez R,Cañal MJ,Jorrín Jdoi
10.1021/pr7006285subject
Has Abstractpub_date
2008-07-01 00:00:00pages
2616-31issue
7eissn
1535-3893issn
1535-3907journal_volume
7pub_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::The Biology/Disease-driven (B/D) working groups of the Human Proteome Project are alliances of research groups aimed at developing or improving proteomic tools to support specific biological or disease-related research areas. Here, we describe the activities and progress to date of the B/D working group focused on pro...
journal_title:Journal of proteome research
pub_type: 杂志文章,评审
doi:10.1021/acs.jproteome.8b00401
更新日期:2018-12-07 00:00:00
abstract::Clinical trials have been conducted for the neuronal ceroid lipofuscinoses (NCLs), a group of neurodegenerative lysosomal diseases that primarily affect children. Whereas clinical rating systems will evaluate long-term efficacy, biomarkers to measure short-term response to treatment would be extremely valuable. To ide...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00460
更新日期:2017-10-06 00:00:00
abstract::Acute kidney injury (AKI) is a frequent complication after cardiopulmonary bypass, but early detection of postoperative AKI remains challenging. Protein biomarkers predict AKI excellently in homogeneous cohorts but are less reliable in patients suffering from various comorbidities. We employed nuclear magnetic resonan...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00219
更新日期:2015-07-02 00:00:00
abstract::Ion mobility-mass spectrometry (IM-MS) is a useful technique for determining information about analyte ion conformation in addition to mass/charge ratio. The physical principles that govern the mobility of an ion through a gas in the presence of a uniform electric field are well understood, enabling rotationally avera...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr3005327
更新日期:2012-11-02 00:00:00
abstract::A major source of intestinal metabolites results from both host and microbial processing of dietary nutrients. (1)H NMR-based metabolic profiling of mouse feces was carried out over time in different microbiome mouse models, including conventional (n = 9), conventionalized (n = 10), and "humanized" gnotobiotic mice in...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr100554m
更新日期:2010-10-01 00:00:00
abstract::Protein phosphorylation is a major mechanism of signal transduction in bacteria. Here, we analyzed the proteome and phosphoproteome of a wild-type strain of the food-borne pathogen Listeria monocytogenes that was grown in either chemically defined medium or rich medium containing glucose. We then compared these result...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr500929u
更新日期:2014-12-05 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::Mass spectrometry (MS)-based proteomics is rapidly emerging as a viable technology for the identification and quantitation of biological samples, such as human plasma--the most complex yet commonly employed biofluid in clinical analyses. The transition from a qualitative to quantitative science is required if proteomi...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr300893w
更新日期:2013-01-04 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::To assess the global effect of preterm birth on fetal metabolism and maternal-fetal nutrient transfer, we used a mass spectrometric-based chemical phenotyping approach on cord blood obtained at the time of birth. We sampled umbilical venous, umbilical arterial, and maternal blood from mothers delivering very-low birth...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr400122v
更新日期:2013-06-07 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::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::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::To estimate the potential of the state-of-the-art proteomics technologies on full coverage of the encoding gene products, the Chinese Human Chromosome Proteome Consortium (CCPC) applied a multiomics strategy to systematically analyze the transciptome, translatome, and proteome of the same cultured hepatoma cells with ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr4009018
更新日期:2014-01-03 00:00:00
abstract::The SEQUEST program was the first and remains one of the most widely used tools for assigning a peptide sequence within a database to a tandem mass spectrum. The cross correlation score is the primary score function implemented within SEQUEST and it is this score that makes the tool particularly sensitive. Unfortunate...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr800420s
更新日期:2008-10-01 00:00:00
abstract::Beta-thalassemia results from mutations of the β-hemoglobin (Hbb) gene and reduced functional Hbb synthesis. Excess α-Hb causes globin chain aggregation, oxidation, cytoskeletal damage, and increased red blood cell clearance. These events result in anemia, altered iron homeostasis, and expansion of extramedullary eryt...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr5010778
更新日期:2015-02-06 00:00:00
abstract::The plasma of patients with stable carotid atherosclerosis (n = 9), and healthy subjects (n = 10) have been fingerprinted with both GC-MS and (1)H NMR. Principal component analysis (PCA), partial least-squares-discriminant analysis (PLS-DA) and orthogonal partial least-squares-discriminant analysis (OPLS-DA) have been...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900668v
更新日期:2009-12-01 00:00:00
abstract::Ozone (O3), a potent air pollutant and a significant greenhouse gas, has been recognized as a major component of global climate change. However, current increasing trends in its background level are projecting a more severe threat to natural and cultivated plants in the near future. The present study has been designed...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr1002824
更新日期:2010-09-03 00:00:00
abstract::The GalNAc O-glycosylation on Ser/Thr residues of extracellular proteins has not been well characterized from a proteomics perspective. We previously reported a sialic acid capture-and-release protocol to enrich tryptic N- and O-glycopeptides from human cerebrospinal fluid glycoproteins using nano-LC-ESI-MS/MS with co...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr300963h
更新日期:2013-02-01 00:00:00
abstract::Protein phosphorylation is essential for numerous cellular processes. Large-scale profiling of phosphoproteins continues to enhance the depth and speed at which we understand these processes. The development of effective phosphoprotein and peptide enrichment techniques and improvements to mass spectrometric instrument...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060559j
更新日期:2007-03-01 00:00:00
abstract::Many proteins can be modified by multiple types of post-translational modifications (Mtp-proteins). Although some post-translational modifications (PTMs) have recently been found to be associated with life-threatening diseases like cancers and neurodegenerative disorders, the underlying mechanisms remain enigmatic to ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr401019d
更新日期:2014-06-06 00:00:00
abstract::Staphylococcus aureus with spa-type t437 has been identified as a predominant community-associated methicillin-resistant S. aureus clone from Asia, which is also encountered in Europe. Molecular typing has previously shown that t437 isolates are highly similar regardless of geographical regions or host environments. T...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00179
更新日期:2019-07-05 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::In Ralstonia eutropha H16, seven genes encoding proteins being involved in the phosphoenolpyruvate-carbohydrate phosphotransferase system (PEP-PTS) were identified. In order to provide more insights into the poly(3-hydroxybutyrate) (PHB)-leaky phenotype of the HPr/EI deletion mutants H16ΔptsH, H16ΔptsI, and H16ΔptsHI ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr300042f
更新日期:2012-07-06 00:00:00
abstract::The intake of 3,4-methylenedioxymethamphetamine (MDMA) is known to increase several endogenous substances involved in steroid and inflammation pathways. Untargeted metabolomics screening approaches can determine biochemical changes after drug exposure and can reveal new pathways, which might be involved in the pharmac...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00438
更新日期:2018-08-03 00:00:00
abstract::This study presents a comparative proteomic analysis of the membrane subproteome of whole Arabidopsis seedlings using 2% Brij-58 or 60% methanol to enrich and solubilize membrane proteins for strong cation exchange fractionation and reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 4...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060525b
更新日期:2007-05-01 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::In-source fragmentation occurs as a byproduct of electrospray ionization. We find that ions produced as a result of in-source fragmentation often match fragment ions produced during MS/MS fragmentation, and we take advantage of this phenomenon in a novel algorithm to analyze LC-MS metabolomics data sets. Our approach ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00601
更新日期:2019-02-01 00:00:00
abstract::Leukocytes play an important role in the progression of disease and leukocyte-derived proteins are associated with the pathogenesis of the disease. Leukocyte activation causes production of inflammatory mediators, over-expression of cell surface adhesion molecules, and an increase in migration and infiltration, phagoc...
journal_title:Journal of proteome research
pub_type: 杂志文章,评审
doi:10.1021/pr0499601
更新日期:2004-09-01 00:00:00