Abstract：
:Transfer ribonucleic acid (tRNA) is the non-coding RNA that links the processes of gene transcription with protein translation. While tRNAs have, individually, been studied for many years, few approaches exist for the global identification of tRNAs at the RNA and posttranscriptional RNA levels. Previously our lab introduced the concept of signature enzymatic digestion products (SDPs) for tRNA identification using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). SDPs enable the direct determination of tRNA identity based on mass spectrometry detection of unique m/z values from enzymatic digestion products. Here we have examined the applicability of liquid chromatography-mass spectrometry (LC-MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS) for global identification of bacterial tRNAs via their SDPs using Escherichia coli as the model system. Optimal ultra high performance and high performance liquid chromatography (UPLC vs. HPLC) conditions were identified to address the hundreds of enzymatic digestion products present in the sample. The use of LC-MS/MS improves the accuracy of SDP assignments through confirming sequence information. The combination of mass unique SDP detection along with MS/MS sequencing yielded the identification of all tRNA families from E. coli and nearly doubles the number of specific SDPs detected over that previously obtained using MALDI-MS. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
journal_name
J Proteomicsjournal_title
Journal of proteomicsauthors
Wetzel C,Limbach PAdoi
10.1016/j.jprot.2011.09.015subject
Has Abstractpub_date
2012-06-27 00:00:00pages
3450-64issue
12eissn
1874-3919issn
1876-7737pii
S1874-3919(11)00454-4journal_volume
75pub_type
杂志文章abstract：:Thioredoxins are ubiquitous disulfide reductases involved in a wide range of cellular processes including DNA synthesis, oxidative stress response and apoptosis. In cereal seeds thioredoxins are proposed to facilitate the germination process by reducing disulfide bonds in storage proteins and other targets in the star...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2010.01.007
更新日期：2010-04-18 00:00:00
abstract：:Xenotropic murine leukemia virus-related virus (XMRV) is a virus generated under artificial conditions by the recombination of 2 murine leukemia virus (MLV) proviruses, PreXMRV-1 and PreXMRV-2, during the in vivo passage of human prostate cancer cells in athymic nude mice. The molecular etiology of XMRV infection has ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.05.047
更新日期：2012-08-03 00:00:00
abstract：UNLABELLED:Phyllomedusine frogs are an extraordinary source of biologically active peptides. At least 8 families of antimicrobial peptides have been reported in this frog clade, the dermaseptins being the most diverse. By a peptidomic approach, integrating molecular cloning, Edman degradation sequencing and tandem mass...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.06.017
更新日期：2016-09-02 00:00:00
abstract：UNLABELLED:The kinetoplastid protozoan parasite, Leishmania donovani, is the causative agent of kala azar or visceral leishmaniasis. Kala azar is a severe form of leishmaniasis that is fatal in the majority of untreated cases. Studies on proteomic analysis of L. donovani thus far have been carried out using homology-ba...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.04.021
更新日期：2014-01-31 00:00:00
abstract：UNLABELLED:The aim of this study was to search for immunogenic schistosomula proteins in the hope of identifying novel intervention targets. Schistosomula proteins were analyzed by immunoproteomic which the probes were sera derived from BALB/c mice (susceptible hosts) and Microtus fortis (resistant hosts). A total of 1...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.04.010
更新日期：2015-06-21 00:00:00
abstract：:For survival, parasite exerts several lines of defense of which drug neutralization is one of the major phenomena. Lack of phase I cytochrome P450 in some of the nematode render them depend on the phase II detoxification system involving GST as a major detoxifying enzymes. In present study, the antifilarial DEC, pheno...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.04.020
更新日期：2011-08-24 00:00:00
abstract：UNLABELLED:Dilated cardiomyopathy (DCM) is a severe heart disease characterized by progressive ventricular dilation and impaired systolic function of the left ventricle. We recently identified a novel pathogenic mutation in the LMNA gene in a family affected by DCM showing sudden death background. We now aimed to ident...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.07.020
更新日期：2016-10-04 00:00:00
abstract：:Jasmonates (JAs) are important phytohormones that regulate a wide range of plant processes, including growth, development and stress responses. Jasmonate ZIM-domain (JAZ) proteins are transcriptional repressors in JA signaling. Overexpression of JAZ7 was found to confer drought tolerance in Arabidopsis thaliana (A. th...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.02.001
更新日期：2019-03-30 00:00:00
abstract：:Growth hormone (GH) promotes longitudinal growth and bone mineralization. In this study, a proteomic approach was used to analyze the association between serum protein expression pattern and height-adjusted bone mineralization in short prepubertal children receiving GH treatment. Patterns of protein expression were co...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2010.08.007
更新日期：2011-01-01 00:00:00
abstract：:Parasitic diseases have a great impact in human and animal health. The gold standard for the diagnosis of the majority of parasitic infections is still conventional microscopy, which presents important limitations in terms of sensitivity and specificity and commonly requires highly trained technicians. More accurate m...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2015.12.030
更新日期：2016-03-16 00:00:00
abstract：:One of the deadly hallmarks of cancer is its ability to prosper within the constraints of the host immune system. Recent advances in immunoproteomics and high-throughput technologies have lead to profiling of the antibody repertoire in cancer patients. This in turn has lead to the identification of tumour associated a...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2012.01.021
更新日期：2012-08-03 00:00:00
abstract：:Protein phosphorylation plays a pivotal role in the regulation of many cellular events; increasing evidences indicate that this post-translational modification is involved in plant response to various abiotic and biotic stresses. Since phosphorylated proteins may be present at low abundance, enrichment methods are gen...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.05.016
更新日期：2011-09-06 00:00:00
abstract：UNLABELLED:Male infertility of cattleyak due to spermatogenic arrest greatly restricts their effective utilization in yak breeding. Although much work has been done to investigate the mechanisms of spermatogenic arrest, there is no information regarding the differences of protein composition between cattleyak and yak t...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.04.049
更新日期：2016-06-16 00:00:00
abstract：:We carried out a comparative proteomic study to explore the molecular mechanisms that underlie the defense response of Douglas-fir (DF, Pseudotsuga menziesii) to laminated root rot, a disease caused by Phellinus sulphurascens. 2-DE was conducted on proteins extracted from roots of laboratory-grown, young DF seedlings ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2008.06.004
更新日期：2008-10-07 00:00:00
abstract：UNLABELLED:Mapping protein-protein interactions for chromatin-associated proteins remains challenging. Here we explore the use of BioID, a proximity biotinylation approach in which a mutated biotin ligase (BirA*) is fused to a bait of interest, allowing for the local activation of biotin and subsequent biotinylation of...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.09.011
更新日期：2015-04-06 00:00:00
abstract：:Dufour's gland is associated with the venom apparatuses of social wasps and bees. This location and its evolutionary adaptations indicate that it could be involved in the production of alarm pheromones in the social wasp Polybia paulista. To investigate this hypothesis, the volatile composition of this gland was analy...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.01.009
更新日期：2017-01-16 00:00:00
abstract：:Gluten proteins are major determinants of the bread making quality of wheat, but also of important wheat-related disorders, including coeliac disease (CD), and allergies. We carried out a proteomic study using the total grain proteins from two low-gliadin wheat lines, obtained by RNAi, and the untransformed wild type ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2017.06.010
更新日期：2017-08-08 00:00:00
abstract：:Quantitative proteomic comparisons require a sufficient number of samples to reach an acceptable level of significance. But 2D gel electrophoresis commonly results in incomplete data sets due to spots with missing values reducing thereby the number of parallel measurements for individual proteins. Here we investigated...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.12.019
更新日期：2012-03-16 00:00:00
abstract：UNLABELLED:Isotopic labeling and isobaric labeling are two kinds of the typical quantification method that have been widely used in proteomics analysis. Herein, a novel quantitative strategy, partially isobaric peptide termini labeling (PITL), was developed to overcome the drawbacks of each above-mentioned labeling str...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.11.014
更新日期：2015-01-30 00:00:00
abstract：:Jasmonate ZIM-domain (JAZ) proteins are key transcriptional repressors regulating various biological processes. Although many studies have studied JAZ proteins by genetic and biochemical analyses, little is known about JAZ7-associated global protein networks and how JAZ7 contributes to bacterial pathogen defense. In t...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.01.002
更新日期：2018-03-20 00:00:00
abstract：UNLABELLED:To further elucidate the molecular mechanism of cytoplasmic male sterility (CMS) in soybean, a differential proteomic analysis was completed between the CMS line NJCMS1A and its maintainer NJCMS1B using iTRAQ-based strategy. As a result, 180 differential abundance proteins (DAPs) were identified, of which, 6...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.02.017
更新日期：2016-04-14 00:00:00
abstract：:Dystrobrevin is a dystrophin-related component of the dystrophin-associated protein complex (DAPC). Using alpha-dystrobrevin as indicator, we aimed to elucidate the interaction network of the DAPC with other proteins during apoptosis of promyelocytic HL-60 cells. The precise role(s) of DBs are not known, but we and ot...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.03.041
更新日期：2012-06-18 00:00:00
abstract：:The Estuarine stonefish (Synanceia horrida) is recognised as one of the most venomous fish species in the world but the overall venom composition has yet to be investigated using in-depth transcriptomic and proteomic methods. To date, known venom components are restricted to a hyaluronidase and a large, pore-forming t...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.04.002
更新日期：2019-06-15 00:00:00
abstract：UNLABELLED:The endocrine role of adipose tissue and its involvement in several physiological and pathological processes are well recognized. Studies on human, mouse and rat adipose tissues have made clear that subcutaneous and visceral deposits play different roles, which is also reflected by different protein and gene...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.05.027
更新日期：2014-08-28 00:00:00
abstract：:Many scorpion accidents occur in the Brazilian Amazonian region and are frequently caused by Tityus obscurus. Approximately 5% of the crude venom of this species is composed of short linear, non-disulfide-bridged peptides, which have not been intensively investigated. As a consequence, only a few of these peptides hav...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2017.09.006
更新日期：2018-01-06 00:00:00
abstract：:The application of silkworm hybrids have promoted the innovation and development of agricultural technology, but the mechanism of heterosis in silkworm has not been explained clearly. In this study, the heterosis of silkworm in the aspects of body weight, silk gland and cocoon weight was investigated by means of silkw...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.103941
更新日期：2020-10-30 00:00:00
abstract：:Wilson's disease is a rare inherited disorder of copper metabolism, manifesting hepatic, neurological and psychiatric symptoms. Early diagnosis is often unfeasible and a unique diagnostic test is currently inapplicable. We performed the qualitative/quantitative characterization of the salivary proteome/peptidome of 32...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.07.033
更新日期：2015-10-14 00:00:00
abstract：:One of the main concerns about genetically modified foods and their potential impacts on human health is that the introduction of a new/ altered gene may putatively alter the expression of others, namely endogenous allergens. We intended to evaluate, and to compare, using quantitative real time RT-PCR technique, the e...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.01.005
更新日期：2012-04-03 00:00:00
abstract：:Gel electrophoresis-based and shotgun approaches are the most employed proteomic platforms in plant biology research, with the latter replacing the former in the last years. We have compared 2-DE-MALDI-TOF/TOF and GeLC-Orbitrap/MS analyses using the same protein extracts from Quercus ilex cotyledons at different devel...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.104087
更新日期：2021-02-20 00:00:00
abstract：:Salinity is one of the major environmental constraints limiting yield of crop plants in many semi-arid and arid regions around the world. To understand responses in soybean seedling to salt stress at proteomic level, the extracted proteins from seedling leaves of salt-sensitive genotype Jackson and salt-tolerant genot...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.11.026
更新日期：2012-02-16 00:00:00
