Abstract:
:Global gel-free proteomic analysis by mass spectrometry has been widely used as an important tool for exploring complex biological systems at the whole genome level. Simultaneous analysis of a large number of protein species is a complicated and challenging task. The challenges exist throughout all stages of a global gel-free proteomic analysis: experimental design, peptide/protein identification, data preprocessing and normalization, and inferential analysis. In addition to various efforts to improve the analytical technologies, statistical methodologies have been applied in all stages of proteomic analyses to help extract relevant information efficiently from large proteomic datasets. In this review, we summarize current applications of statistics in several stages of global gel-free proteomic analysis by mass spectrometry. We discuss the challenges associated with the applications of various statistical tools. Whenever possible, we also propose potential solutions on how to improve the data collection and interpretation for mass-spectrometry-based global proteomic analysis using more sophisticated and/or novel statistical approaches.
journal_name
Crit Rev Biotechnoljournal_title
Critical reviews in biotechnologyauthors
Nie L,Wu G,Zhang Wdoi
10.1080/07388550802543158subject
Has Abstractpub_date
2008-01-01 00:00:00pages
297-307issue
4eissn
0738-8551issn
1549-7801pii
905979708journal_volume
28pub_type
杂志文章,评审abstract::Butanol is a precursor of many industrial chemicals, and a fuel that is more energetic, safer and easier to handle than ethanol. Fermentative biobutanol can be produced using renewable carbon sources such as agro-industrial residues and lignocellulosic biomass. Solventogenic clostridia are known as the most preeminent...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388551.2017.1376308
更新日期:2018-05-01 00:00:00
abstract::The role of selenium (Se) in human health and diseases has been discussed in detail in several recent reviews, with the main conclusion being that selenium deficiency is recognised as a global problem which urgently needs resolution. Since selenium content in plant-based food depends on its availability from soil, the...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388550802658030
更新日期:2009-01-01 00:00:00
abstract::Many reporter genes, such as gfp, gusA, and lacZ, are widely used for research into plants, animals, and microorganisms. Reporter genes, which offer high levels of sensitivity and convenience of detection, have been utilized in transgenic technology, promoter analysis, drug screening, and other areas. Directed molecul...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2011.593503
更新日期:2012-06-01 00:00:00
abstract::Microbial diversity provides an immense reservoir of functions and supports key steps in maintaining ecosystem balance through matter decomposition processes and nutrient recycling. The use of microorganisms for biomolecule production is now common, but often involves single-strain cultures. In this review, we highlig...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2015.1100584
更新日期:2017-02-01 00:00:00
abstract::Microbial bio-transformations of the essential trace element selenium are now recognized to occur among a wide variety of microorganisms. These transformations are used to convert this element into its assimilated form of selenocysteine, which is at the active center of a number of key enzymes, and to produce selenium...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章
doi:10.1080/07388551.2020.1811199
更新日期:2020-12-01 00:00:00
abstract::Affinity tags are vital tools for the production of high-throughput recombinant proteins. Several affinity tags, such as the hexahistidine tag, maltose-binding protein, streptavidin-binding peptide tag, calmodulin-binding peptide, c-Myc tag, glutathione S-transferase and FLAG tag, have been introduced for recombinant ...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2016.1163323
更新日期:2017-05-01 00:00:00
abstract::Arbuscular mycorrhizal fungi (AMF) form widespread symbiotic associations with 80% of known land plants. They play a major role in plant nutrition, growth, water absorption, nutrient cycling and protection from pathogens, and as a result, contribute to ecosystem processes. Salinity stress conditions undoubtedly limit ...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2014.899964
更新日期:2015-01-01 00:00:00
abstract::Protein glycosylation is post-translational modification (PTM) which is important for pharmacokinetics and immunogenicity of recombinant glycoprotein therapeutics. As a result of variations in monosaccharide composition, glycosidic linkages and glycan branching, glycosylation introduces considerable complexity and het...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388551.2017.1416577
更新日期:2018-09-01 00:00:00
abstract::The Vitamin K series, particularly menaquinone, have been attracting research attention, due to the potential in reducing both osteoporosis and cardiovascular diseases. This review provides an overview of the types of vitamin K and their health benefits. This is followed by a critical review of the various biotechnolo...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2013.832142
更新日期:2015-06-01 00:00:00
abstract::Semisynthetic cephalosporins are important antibacterials in clinical practice. Semisynthetic cephalosporins are manufactured by derivatizing 7-aminocephalosporanic acid (7-ACA) and its desacetylated form. Microbial enzymes such as D-amino acid oxidase, glutaryl-7-ACA acylase and cephalosporin esterase are being used ...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388550600718630
更新日期:2006-04-01 00:00:00
abstract::Cross-linked enzyme aggregate (CLEA) technology has been regarded as an effective carrier-free immobilization method. This method is very attractive due to its simplicity and robustness, as well as for the possibility of using the crude enzyme extract and the opportunity to co-immobilize multiple different enzymes. Th...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2013.795516
更新日期:2015-03-01 00:00:00
abstract::Natural cellular microenvironment consists of spatiotemporal gradients of multiple physical (e.g. extracellular matrix stiffness, porosity and stress/strain) and chemical cues (e.g. morphogens), which play important roles in regulating cell behaviors including spreading, proliferation, migration, differentiation and a...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2014.993588
更新日期:2016-01-01 00:00:00
abstract::The acetic acid bacteria (AAB) have important roles in food and beverage production, as well as in the bioproduction of industrial chemicals. In recent years, there have been major advances in understanding their taxonomy, molecular biology, and physiology, and in methods for their isolation and identification. AAB ar...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388550802046749
更新日期:2008-01-01 00:00:00
abstract::Salt-tolerant plants grow in a wide variety of saline habitats, from coastal regions, salt marshes and mudflats to inland deserts, salt flats and steppes. Halophytes living in these extreme environments have to deal with frequent changes in salinity level. This can be done by developing adaptive responses including th...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2011.630647
更新日期:2012-12-01 00:00:00
abstract::Starting with a brief history of solid-state fermentation (SSF), major aspects of SSF are reviewed, which include factors affecting SSF, biomass, fermentors, modeling, industrial microbial enzymes, organic acids, secondary metabolites, and bioremediation. Physico-chemical and environmental factors such as inoculum typ...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388550590925383
更新日期:2005-01-01 00:00:00
abstract::The 2014 Ebola outbreak, the largest recorded, took us largely unprepared, with no available vaccine or specific treatment. In this context, the World Health Organization declared that the humanitarian use of experimental therapies against Ebola Virus (EBOV) is ethical. In particular, an experimental treatment consist...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2015.1114465
更新日期:2017-02-01 00:00:00
abstract::Recombinant DNA technology enables the creation of well-defined alterations in the genetic material of an organism. Methods to manipulate recombinant DNA in the filamentous fungi (a group of microorganisms that includes species of academic as well as commercial interest) have recently been developed. This has been the...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388558709089387
更新日期:1987-01-01 00:00:00
abstract::Grapes are one of the most cultivated fruit crops worldwide. Either for wine or juice production, grape processing generates a large amount of residues that must be treated, disposed of or reused properly to reduce their pollution load before being applied to the soil. In this review, a special focus is given to the t...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章
doi:10.1080/07388551.2018.1555514
更新日期:2019-06-01 00:00:00
abstract::The enzyme α-galactosidase (α-D-galactoside galactohydrolase; EC 3.2.1.22) catalyzes the hydrolysis of α-1,6-linked galactose residues in oligosaccharides and polymeric galactomannan. The α-galactosidases are of particular interest in view of their many potential biotechnological and medical applications. These enzyme...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2013.794124
更新日期:2014-12-01 00:00:00
abstract::Metabolic engineering is crucial in the development of production strains for platform chemicals, pharmaceuticals and biomaterials from renewable resources. The central carbon metabolism (CCM) of heterotrophs plays an essential role in the conversion of biomass to the cellular building blocks required for growth. Yet,...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章
doi:10.1080/07388551.2020.1785386
更新日期:2020-11-01 00:00:00
abstract::Cancer is a clinical situation caused by uncontrolled cell division and is responsible for a large number of deaths worldwide. Colchicine is a classical antimitotic, tubulin-binding agent (TBA) which is being explored for its antitumor activities, although its tubulin-binding ability leads to some toxicity toward norm...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388551.2017.1303804
更新日期:2017-12-01 00:00:00
abstract::Endocrine-disrupting compounds (EDCs) can interfere with endocrine systems and bio-accumulate through the food chain and even decrease biodiversity in contaminated areas. This review discusses a critical overview of recent research progress in the biotransformation of EDCs (including polychlorinated biphenyl and nonyl...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388551.2017.1386613
更新日期:2018-08-01 00:00:00
abstract::Over the past few decades, a considerable attention has been focused on the microbial polyhydroxyalkanoates (PHAs) owing to its multifaceted properties, i.e. biodegradability, biocompatibility, non-toxicity and thermo-plasticity. This article presents a critical review of the foregoing research, current trends and fut...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2014.913548
更新日期:2015-01-01 00:00:00
abstract::Cypripedium orchids have high horticultural value. The populations of most species are very geographically restricted and they are becoming increasingly rare due to the destruction of native habitats and illegal collection. Reduction of the commercial value through large-scale propagation in vitro is a preferable opti...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.3109/07388551.2013.841117
更新日期:2014-12-01 00:00:00
abstract::l-Leucine, as an essential branched-chain amino acid for humans and animals, has recently been attracting much attention because of its potential for a fast-growing market demand. The applicability ranges from flavor enhancers, animal feed additives and ingredients in cosmetic to specialty nutrients in pharmaceutical ...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388551.2019.1577214
更新日期:2019-08-01 00:00:00
abstract::Since several decades ago, the application of pervaporation (PV) technology has been mainly aimed at the separation of different types of water-organic, organic-water and organic-organic mixtures, reaching its large-scale application in industry for the dehydration of organics. Today, the versatility and high selectiv...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388551.2019.1631248
更新日期:2019-11-01 00:00:00
abstract::Lipopolysaccharide (LPS), the major component of the outer membrane of Gram-negative bacteria, often pose a serious risk not only when delivered in the bloodstream but also in air, the environment and several industrial fields such as pharmaceutics or food. LPS is constituted of three regions; the O-specific chain, th...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章
doi:10.1080/07388551.2019.1709797
更新日期:2020-05-01 00:00:00
abstract::Bacteriocins produced by lactic acid bacteria (LAB) are well-recognized for their potential as natural food preservatives. These antimicrobial peptides usually do not change the sensorial properties of food products and can be used in combination with traditional preservation methods to ensure microbial stability. In ...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388551.2016.1262323
更新日期:2017-11-01 00:00:00
abstract::Mushrooms have become increasingly important as a reliable food source. They have also been recognized as an important source of bioactive compounds of high nutritional and medicinal values. The nucleobases, nucleosides and nucleotides found in mushrooms play important roles in the regulation of various physiological ...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388551.2017.1399102
更新日期:2018-08-01 00:00:00
abstract::Erythritol is a natural sweetener commonly used in the food and pharmaceutical industries. Produced by microorganisms as an osmoprotectant, it is an ideal sucrose substitute for diabetics or overweight persons due to its almost zero calorie content. Currently, erythritol is produced on an industrial scale through the ...
journal_title:Critical reviews in biotechnology
pub_type: 杂志文章,评审
doi:10.1080/07388551.2017.1380598
更新日期:2018-06-01 00:00:00