Abstract：
:Many powerful analytical techniques for investigation of nucleic acids exist in the average modern molecular biology lab. The current review will focus on questions in RNA biology that have been answered by the use of mass spectrometry, which means that new biological information is the purpose and outcome of most of the studies we refer to. The review begins with a brief account of the subject "MS in the biology of RNA" and an overview of the prevalent RNA modifications identified to date. Fundamental considerations about mass spectrometric analysis of RNA are presented with the aim of detailing the analytical possibilities and challenges relating to the unique chemical nature of nucleic acids. The main biological topics covered are RNA modifications and the enzymes that perform the modifications. Modifications of RNA are essential in biology, and it is a field where mass spectrometry clearly adds knowledge of biological importance compared to traditional methods used in nucleic acid research. The biological applications are divided into analyses exclusively performed at the building block (mainly nucleoside) level and investigations involving mass spectrometry at the oligonucleotide level. We conclude the review discussing aspects of RNA identification and quantifications, which are upcoming fields for MS in RNA research. 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
Giessing AM,Kirpekar Fdoi
10.1016/j.jprot.2012.01.032subject
Has Abstractpub_date
2012-06-27 00:00:00pages
3434-49issue
12eissn
1874-3919issn
1876-7737pii
S1874-3919(12)00072-3journal_volume
75pub_type
杂志文章,评审abstract：UNLABELLED:Dietary fiber/starch imbalance can lead to diarrhea in rabbits. However, the underlying molecular mechanisms are largely unknown, and this is the first study on the proteome profile of the cecal tissue of diarrheic rabbits. In this study, one group of weanling rabbits was fed a high fiber/starch diet (contro...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.03.019
更新日期：2014-05-30 00:00:00
abstract：:Lactobacillus fermentum is a natural resident of the human GIT and is used as a probiotic. A unique property of L. fermentum is its ability to tolerate, colonize, and survive in the harsh conditions of bile, which facilitates transient colonization of the host colon. In the current study, we investigated the key mecha...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103600
更新日期：2020-02-20 00:00:00
abstract：:No effective screening method is available for oral squamous cell carcinoma (OSCC) that is recognized to influence by environmental factors as well as human papillomavirus (HPV) and Epstein-Barr virus (EBV). Therefore, we sought to identify salivary biomarkers for screening of OSCC with or without HPV and/or EBV infec...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2017.11.022
更新日期：2018-02-20 00:00:00
abstract：:Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) is a rapid methodology for identification of bacteria that is increasingly used in diagnostic laboratories. This work aimed at evaluating the potential of MALDI-TOF-MS for identification of the main serotypes of Flavobacterium ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2017.09.007
更新日期：2018-01-06 00:00:00
abstract：:In this study, we performed an integrated physiological and chloroplast proteome analysis of wheat seedling leaves under salt and osmotic stresses by label-free based quantitative proteomic approach. Both salt and osmotic stresses significantly increased the levels of abscisic acid and methyl jasmonate and led to dama...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.104097
更新日期：2021-03-15 00:00:00
abstract：:Aggregatability and oxidative damage of red blood cells (RBCs), platelet activation and increased amount of blood cells-derived microparticles (MPs) are thought to be the etiologies for the thrombotic risk in thalassemia, but with unclear mechanisms. Here we report cellular origins and increases in number, oxidative s...
journal_title：Journal of proteomics
pub_type： 临床试验,杂志文章
doi：10.1016/j.jprot.2012.06.004
更新日期：2012-12-05 00:00:00
abstract：:Soil fungistasis limits the effect of fungal agents designed to control plant-parasitic nematodes. Benzaldehyde is a fungistatic factor produced by soil microorganisms that can suppress conidial germination, but the molecular mechanism of this suppression is unknown. In this study, three conidial proteomes of Arthrobo...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.09.016
更新日期：2019-02-10 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：:The biological variance in protein expression of interest to biologists can only be accessed if the technical variance of the protein quantification method is low compared with the biological variance. Technical variance is dependent on the protocol employed within a quantitative proteomics experiment and accumulated ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.09.020
更新日期：2012-12-21 00:00:00
abstract：UNLABELLED:Extracellular vesicles are produced by many pathogenic microorganisms and have varied functions that include secretion and release of microbial factors, which contribute to virulence. Very little is known about vesicle production by Gram-positive bacteria, as well as their biogenesis and release mechanisms. ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.04.023
更新日期：2014-06-25 00:00:00
abstract：:Deciphering Plasmodium vivax biology has long been a challenge for groups working on this parasite, mainly due to the complications involved in propagating it in vitro. However, adapting P. vivax strains in non-human primates and the arrival of high-performance analysis methods has led to increased knowledge regarding...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2020.103719
更新日期：2020-04-30 00:00:00
abstract：:FGF8 specifies early tooth development by directing the migration of the early tooth founder cells to the site of tooth emergence. To date the effect of the FGF8 in adult dental pulp has not been studied. We have assessed the regenerative potential of FGF8 by evaluating changes in the proteome landscape of dental pulp...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.05.004
更新日期：2018-07-15 00:00:00
abstract：:The pre-treatment of biological extracts with the aim of detecting very low-abundance proteins generates complexity requiring a proper fractionation. Therefore the success of identifying all newly detectable species depends on the selected fractionation methods. In this context and starting from a human serum, where t...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2009.06.014
更新日期：2009-08-20 00:00:00
abstract：UNLABELLED:Erwinia amylovora is a Gram-negative plant pathogen that causes fire blight. This disease affects most members of the Rosaceae family including apple and pear. Here, an infection model is introduced to study proteomic changes in a highly virulent E. amylovora strain upon interaction with its host as compared...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.02.018
更新日期：2016-04-29 00:00:00
abstract：:For relative protein quantitation by mass spectrometry we metabolically labeled E. coli bacteria with (15)N-enriched diets. Proteins extracted from (15)N-labeled and unlabeled E. coli bacteria were mixed, separated by two-dimensional gel electrophoresis and enzymatically digested. The resulting tryptic peptides were a...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2008.10.004
更新日期：2009-01-30 00:00:00
abstract：UNLABELLED:This study was conducted to define differences in Fusarium oxysporum f. sp. fragariae (Fof) isolates with different virulence efficiency to strawberry at the proteome level, in combination with their differences in mycelial growth, conidial production and germination. Comparative proteome analyses revealed s...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.05.023
更新日期：2014-08-28 00:00:00
abstract：:In pre-weaning calves, both leucine and threonine play important roles in growth and muscle metabolism. In this study, metabolomics, proteomics and clinical chemistry were used to assess the effects of leucine and threonine supplementation added to milk replacer on 14 newborn Holstein male calves: 7 were fed a control...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.103677
更新日期：2020-03-30 00:00:00
abstract：UNLABELLED:The vacuole is by far the largest multifunctional organelle in fruits and plays a functional role in fruit development and fruit quality. Despite its significance, little information exists pertaining to the role of the vacuolar membrane (tonoplast) in the process of fruit senescence. In the present study, a...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.06.031
更新日期：2016-09-02 00:00:00
abstract：:Neurodegenerative diseases often lack early and specific diagnostic and prognostic biomarkers. Many studies are focusing on the cerebrospinal fluid (CSF) proteome to identify relevant biomarkers and therapeutic targets for these disorders. An alternative approach consists in comparing proteins secreted by healthy neur...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.09.013
更新日期：2012-12-21 00:00:00
abstract：:Termite soldiers constitute the defensive frontline of the colonies, despite workers also perform such tasks, especially within the Neotropical Apicotermitinae, in which all species are soldierless. Workers of the genus Ruptitermes display an extreme form of defense, characterized by body rupture and release of a stic...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103622
更新日期：2020-02-20 00:00:00
abstract：:"Secretome" is referred to as the rich, complex set of molecules secreted from living cells. In a less strict definition frequently followed in "secretome" studies, the term also includes molecules shed from the surface of living cells. Proteins of secretome (will be referred to as secreted) play a key role in cell si...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2010.07.001
更新日期：2010-11-10 00:00:00
abstract：:Gluten, a group of proteins found in wheat, barley, and rye, is the trigger of celiac disease, an immune disorder that affects about 1% of people worldwide. The toxicity of partially hydrolyzed gluten (PHG) in fermented products is less well understood due to the significant analytical challenges in PHG characterizati...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103538
更新日期：2020-01-06 00:00:00
abstract：:Calcium (Ca2+) controls progression through the mammalian cell cycle by engaging a diverse range of molecular pathways. While the essential role of spatio-temporal Ca2+ signalling in the cell cycle is well established, the precise mechanisms by which it regulates cell cycle entry and progression through G1 are not par...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2017.08.006
更新日期：2018-01-06 00:00:00
abstract：UNLABELLED:Secretion of bioactive mediators regulates cell interactions with the microenvironment in tissue homeostasis and wound healing processes. We assessed the cardiomyocyte secretory response to hypoxia with the aim of identifying key mediators of tissue pathology and repair after ischemic heart attack. We profil...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.12.025
更新日期：2014-02-26 00:00:00
abstract：:Flightin is a myosin binding phosphoprotein that originated in the ancestor to Pancrustacea ~500 MYA. In Drosophila melanogaster, flightin is essential for length determination and flexural rigidity of thick filaments. Here, we show that among 12 Drosophila species, the N-terminal region is characterized by low sequen...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.12.006
更新日期：2016-03-01 00:00:00
abstract：:Plasma membrane intrinsic proteins (PIPs) are one subfamily of aquaporins that mediate the transmembrane transport of water. To reveal their function in poplar, we generated transgenic poplar plants in which the translation of PIP genes was downregulated by RNA interference investigated these plants with a comprehensi...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.07.029
更新日期：2015-10-14 00:00:00
abstract：:Early response to 7 days of prednisolone (PRED) treatment is one of the important prognostic factors in predicting eventual outcome in childhood acute lymphoblastic leukemia (ALL). Using proteomic tools and clinically important leukemia cell lines (REH, 697, Sup-B15, RS4; 11), we have identified potential prognostic p...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.02.034
更新日期：2011-05-16 00:00:00
abstract：UNLABELLED:Oleaginous microalgae are capable of producing large quantities of fatty acids and triacylglycerides. As such, they are promising feedstocks for the production of biofuels and bioproducts. Genetic strain-engineering strategies offer a means to accelerate the commercialization of algal biofuels by improving t...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.05.025
更新日期：2013-11-20 00:00:00
abstract：:Ubiquitylation is an elaborate post-translational modification involved in all biological processes. Its pleotropic effect is driven by the ability to form complex polyubiquitin chain architectures that can influence biological functions. In this study, we optimised sample preparation and chromatographic separation of...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.103963
更新日期：2020-10-30 00:00:00
abstract：:Populations of small eukaryotic RNAs, in addition to relatively well recognized molecules such as miRNAs or siRNAs, also contain fragments derived from all classes of constitutively expressed non-coding RNAs. It has been recently demonstrated that the formation and accumulation of RNA fragments (RFs) is cell-/tissue-s...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.10.007
更新日期：2019-02-20 00:00:00
