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1.
Sanz-Medel A Montes-Bayón M del Rosario Fernández de la Campa M Encinar JR Bettmer J 《Analytical and bioanalytical chemistry》2008,390(1):3-16
In the last decade mass-spectrometry-based proteomics has become an indispensable analytical tool for molecular biology, cellular
biology and, lately, for the emerging systems biology. This review summarises the evolution and great potential of analytical
methods based on elemental mass-spectrometric detection for quantitative proteomic analysis. 相似文献
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We report the development of a new reagent, called CILAT (Cleavable Isobaric Labeled Affinity Tag), for quantitative proteomics, which represents an improvement over current ICAT (Isotope-Coded Affinity Tag) and iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) methods. 相似文献
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Playing tag with quantitative proteomics 总被引:1,自引:0,他引:1
There is steady need for new proteomic strategies on quantitative measurements that provide essential components for detailing
dynamic changes in many cellular functions and processes. Stable isotope labeling is a rapidly evolving field, which can be
used either after protein extraction with chemical labeling, or in cell culture with metabolic incorporation. In this review,
we explore the most frequently utilized quantitation techniques with particular attention paid to chemical labeling using
different isotopic tags, including a recent labeling strategy—soluble polymer-based isotopic labeling (SoPIL)—that achieves
efficient labeling in homogeneous conditions. Special care should be devoted to the selection of appropriate quantitation
approaches according to the needs of the sample and overall experimental design. We evaluate recent advances in quantitative
proteomics using stable isotope labeling and their applications to current insightful biological inquiries.
Figure Chemical modules of isotopic tags for quantitative proteomics. 相似文献
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A new deuterated alkylating agent for quantitative proteomics 总被引:3,自引:0,他引:3
Sebastiano R Citterio A Lapadula M Righetti PG 《Rapid communications in mass spectrometry : RCM》2003,17(21):2380-2386
Weakly basic molecules containing a double bond, such as 2- and 4-vinylpyridine, are able to react and selectively alkylate -SH groups in proteins, thus preventing their re-oxidation to disulphide bridges. In contrast to conventional alkylating agents such as iodoacetamide and non-charged acrylamide derivatives, such molecules achieve 100% alkylation of all -SH residues, even in complex proteins, without reacting with other functional groups. Their use is particularly effective in proteome analysis and more generally for analyzing proteins in which the -SH groups should be blocked. Additionally, the use of vinylpyridines, partially or totally deuterated and thus with a mass difference compared with their non-deuterated counterparts of 4-7 Da, allows studies of induction/repression of protein synthesis (quantitative proteomics). 相似文献
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Monica H. Elliott Derek S. Smith Carol E. Parker Christoph Borchers 《Journal of mass spectrometry : JMS》2009,44(12):1637-1660
It was inevitable that as soon as mass spectrometrists were able to tell biologists which proteins were in their samples, the next question would be how much of these proteins were present. This has turned out to be a much more challenging question. In this review, we describe the multiple ways that mass spectrometry has attempted to address this issue, both for relative quantitation and for absolute quantitation of proteins. There is no single method that will work for every problem or for every sample. What we present here is a variety of techniques, with guidelines that we hope will assist the researcher in selecting the most appropriate technique for the particular biological problem that needs to be addressed. We need to emphasize that this is a very active area of proteomics research—new quantitative methods are continuously being introduced and some ‘pitfalls’ of older methods are just being discovered. However, even though there is no perfect technique—and a better technique may be developed tomorrow—valuable information on biomarkers and pathways can be obtained using these currently available methods Copyright © 2009 John Wiley & Sons, Ltd. 相似文献
6.
Magnus Palmblad Yuri E. M. van der Burgt Ekaterina Mostovenko Hans Dalebout André M. Deelder 《Journal of the American Society for Mass Spectrometry》2010,21(6):1002-1011
We have developed and implemented a novel mass spectrometry (MS) platform combining the advantages of high mass accuracy and
resolving power of Fourier transform ion cyclotron resonance (FTICR) with the economy and speed of multiple ion traps for
tandem mass spectrometry. The instruments are integrated using novel algorithms and software and work in concert as one system.
Using chromatographic time compression, a single expensive FTICR mass spectrometer can match the throughput of multiple relatively
inexpensive ion trap instruments. Liquid chromatography (LC)-mass spectrometry data from the two types of spectrometers are
aligned and combined to hybrid datasets, from which peptides are identified using accurate mass from the FTICR data and tandem
mass spectra from the ion trap data. In addition, the high resolving power and dynamic range of a 12 tesla FTICR also allows
precise label-free quantitation. Using two ion traps in parallel with one LC allows simultaneous MS/MS experiments and optimal
application of collision induced dissociation and electrontransfer dissociation throughout the chromatographic separation
for increased proteome coverage, characterization of post-translational modifications and/or simultaneous measurement in positive
and negative ionization mode. An FTICR-ion trap cluster can achieve similar performance and sample throughput as multiple
hybrid ion trap-FTICR instruments, but at a lower cost. We here describe the first such FTICR-ion trap cluster, its performance
and the idea of chromatographic compression. 相似文献
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Zhu H Pan S Gu S Bradbury EM Chen X 《Rapid communications in mass spectrometry : RCM》2002,16(22):2115-2123
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The field of proteomics aims to develop and apply technologies for the characterization of protein function on a global scale. Toward this end, synthetic chemistry has played a major role by providing new reagents to profile segments of the proteome based on activity rather than abundance. Small molecule probes for activity-based protein profiling have been created for more than a dozen enzyme classes and used to discover several enzyme activities elevated in disease states. These innovations have inspired complementary advancements in analytical chemistry, where new platforms have been introduced to augment the information content achievable in chemical proteomics experiments. Here, we will review these analytical platforms and discuss how they have exploited the versatility of chemical probes to gain unprecedented insights into the function of proteins in biological samples of high complexity. 相似文献
12.
The carbonyl-phenol-acid reaction system yields color reactions with phenols, carbonyl compounds (aldehydes and ketones), and inorganic acids. 'I'o test for one of the components of this reaction system, the remaining two components constitute the specific reagents.The four related compounds, pyridoxine, pyridoxamine, pyridoxal, and pyridoxic acid each possess a phenolic hydroxyl. Pyridoxal possesses an aldehyde group in addition to the phenolic hydroxyl. Pyridoxal yields an intense yellow color on treatment with concentrated sulfuric acid. Pyridoxine, pyridoxamine and pyridoxic acid prove not to be chromogenic on treatment with concentrated sulfuric acid. Pyridoxal can therefore be differentiated by means of the sulfuric acid reaction from the other three compounds related to vitamin B6.The colored product obtained by the interaction of pyridoxa1 and concentrated sulfuric acid yields a characteristic absorption spectrum and follows the Beer-Lambert law in the concentrations of pyridoxal tested (l0—100 μg). 相似文献
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A computer-assisted liquid chromatographic system (MCASYST) is evaluated for automatic qualitative and quantitative analysis of toxic drugs in poisoned human fluids. The system performance is confirmed by the actual analyses of several cases of poisoning. The results indicate that the accuracy of identification by retention prediction and UV spectral search is very high, and quantitation by the memorized calibration curves can be performed very conveniently. However, it is difficult at present to identify all peaks that appear in chromatograms for human urine and serum because the drugs may be changed to their metabolites in those fluids. Metabolite identification will be the next step to improve the performance of this system. 相似文献
16.
Geromanos SJ Hughes C Ciavarini S Vissers JP Langridge JI 《Analytical and bioanalytical chemistry》2012,404(4):1127-1139
To accurately determine the quantitative change of peptides and proteins in complex proteomics samples requires knowledge of how well each ion has been measured. The precision of each ions' calculated area is predicated on how uniquely it occupies its own space in m/z and elution time. Given an initial assumption that prior to the addition of the "heavy" label, all other ion detections are unique, which is arguably untrue, an initial attempt at quantifying the pervasiveness of ion interference events in a representative binary SILAC experiment was made by comparing the centered m/z and retention time of the ion detections from the "light" variant to its "heavy" companion. Ion interference rates were determined for LC-MS data acquired at mass resolving powers of 20 and 40 K with and without ion mobility separation activated. An ion interference event was recorded, if present in the companion dataset was an ion within ± its Δ mass at half-height, ±15 s of its apex retention time and if utilized by ±1 drift bin. Data are presented illustrating a definitive decrease in the frequency of ion interference events with each additional increase in selectivity of the analytical workflow. Regardless of whether the quantitative experiment is a composite of labeled samples or label free, how well each ion is measured can be determined given knowledge of the instruments mass resolving power across the entire m/z scale and the ion detection algorithm reporting both the centered m/z and Δ mass at half-height for each detected ion. Given these measurements, an effective resolution can be calculated and compared with the expected instrument performance value providing a purity score for the calculated ions' area based on mass resolution. Similarly, chromatographic and drift purity scores can be calculated. In these instances, the error associated to an ions' calculated peak area is estimated by examining the variation in each measured width to that of their respective experimental median. Detail will be disclosed as to how a final ion purity score was established, providing a first measure of how accurately each ions' area was determined as well as how precise the calculated quantitative change between labeled or unlabelled pairs were determined. Presented is how common ion interference events are in quantitative proteomics LC-MS experiments and how ion purity filters can be utilized to overcome and address them, providing ultimately more accurate and precise quantification results across a wider dynamic range. 相似文献
17.
Critical survey of quantitative proteomics in two-dimensional electrophoretic approaches 总被引:1,自引:0,他引:1
Righetti PG Castagna A Antonucci F Piubelli C Cecconi D Campostrini N Antonioli P Astner H Hamdan M 《Journal of chromatography. A》2004,1051(1-2):3-17
The present review attempts to cover a number of methods that appeared in the last few years for performing quantitative proteome analysis. However, due to the large number of methods described for both electrophoretic and chromatographic approaches, we have limited this excursus only to conventional two-dimensional (2D) map analysis, coupling orthogonally a charge-based step (isoelectric focusing) to a size-based separation (sodium dodecyl sulfate (SDS)-electrophoresis). The first and oldest method applied in 2D mapping is based on statistical analysis performed on sets of gels via powerful software packages, such as the Melanie, PDQuest, Z3 and Z4000, Phoretix and Progenesis. This method calls for separately-running a number of replicas for control and treated samples, the merging and comparing between these two sets of data being accomplished via the softwares just mentioned. Recent developments permit analyses on a single gel containing mixed samples differentially labelled and resolved by either fluorescence or isotopic means. In one approach, a set of fluorophors, called Cy3 and Cy5, are selected for differentially tagging Lys residues, via a "minimal labelling" protocol. A variant of this, adopts a newer set of fluorophors, also of the Cy3 and Cy5 type, reacting on Cys residues, via a strategy of "saturation labelling". There are at present two methods for quantitative proteomics in a 2D gel format exploiting stable isotopes: one utilizes tagging Cys residues with [2H0]/[2H3]-acrylamide; the other one, also based on a Cys reactive compound, exploits [2H0]/[2H4] 2-vinylpyridine. The latter reagent achieves 100% efficiency coupled to 100% specificity. The advantages and limitations of the various protocols are discussed. 相似文献
18.
The discovery of various protein/receptor targets from genomic research is expanding rapidly. Along with the automation of organic synthesis and biochemical screening, this is bringing a major change in the whole field of drug discovery research. In the traditional drug discovery process, the industry tests compounds in the thousands. With automated synthesis, the number of compounds to be tested could be in the millions. This two-dimensional expansion will lead to a major demand for resources, unless the chemical libraries are made wisely. The objective of this work is to provide both quantitative and qualitative characterization of known drugs which will help to generate "drug-like" libraries. In this work we analyzed the Comprehensive Medicinal Chemistry (CMC) database and seven different subsets belonging to different classes of drug molecules. These include some central nervous system active drugs and cardiovascular, cancer, inflammation, and infection disease states. A quantitative characterization based on computed physicochemical property profiles such as log P, molar refractivity, molecular weight, and number of atoms as well as a qualitative characterization based on the occurrence of functional groups and important substructures are developed here. For the CMC database, the qualifying range (covering more than 80% of the compounds) of the calculated log P is between -0.4 and 5.6, with an average value of 2.52. For molecular weight, the qualifying range is between 160 and 480, with an average value of 357. For molar refractivity, the qualifying range is between 40 and 130, with an average value of 97. For the total number of atoms, the qualifying range is between 20 and 70, with an average value of 48. Benzene is by far the most abundant substructure in this drug database, slightly more abundant than all the heterocyclic rings combined. Nonaromatic heterocyclic rings are twice as abundant as the aromatic heterocycles. Tertiary aliphatic amines, alcoholic OH and carboxamides are the most abundant functional groups in the drug database. The effective range of physicochemical properties presented here can be used in the design of drug-like combinatorial libraries as well as in developing a more efficient corporate medicinal chemistry library. 相似文献
19.
E. Wiegand 《Fresenius' Journal of Analytical Chemistry》1966,222(4):445-446
Ohne Zusammenfassung 相似文献
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Kovanich D Cappadona S Raijmakers R Mohammed S Scholten A Heck AJ 《Analytical and bioanalytical chemistry》2012,404(4):991-1009
Mass spectrometry has proven to be an indispensable tool for protein identification, characterization, and quantification. Among the possible methods in quantitative proteomics, stable isotope labeling by using reductive dimethylation has emerged as a cost-effective, simple, but powerful method able to compete at any level with the present alternatives. In this review, we briefly introduce experimental and software methods for proteome analysis using dimethyl labeling and provide a comprehensive overview of reported applications in the analysis of (1) differential protein expression, (2) posttranslational modifications, and (3) protein interactions. 相似文献