New separation tools for comprehensive studies of protein expression by mass spectrometry

Nilsson, Carol L.; Davidsson, Pia

doi:10.1002/1098-2787(2000)19:6<390::aid-mas2>3.0.co;2-1

Cited by 42 publications

(26 citation statements)

References 47 publications

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“…Proteomics can provide the researcher with more than the hypothetical cellular scenario. With a well-designed experiment, investigators can examine the conditions under which a protein is expressed (Nilsson & Davidson 2000, Kislinger & Emili 2003, its cellular location (Dunkley et al 2004), the relative quantities (Yao et al 2001, Molloy et al 2005, and what protein-protein interactions take place (Giot et al 2003, Schweitzer et al 2003.…”

Section: Using Proteomics To Complement Genomic Findings In Marine Ecmentioning

confidence: 99%

Marine proteomics

Nunn¹,

Timperman²

2007

Mar. Ecol. Prog. Ser.

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A wealth of information is recorded in a protein's primary sequence, which can be used to determine its biological function and origin, and provide clues to the mechanisms of degradation. In contrast to DNA, proteins and their amino acid constituents have demonstrated a wide-spread presence outside the cell, preserved in the environment. In marine samples, proteins are present as mixtures from numerous sources in a salty, complex matrix at low concentrations. As a result of these factors, studies of this nitrogen-based component in the oceans have previously been limited to bulk elemental and amino acid analyses; these analyses were incapable of providing details regarding protein sequence, function and source information. Advances in biological mass spectrometry now allow for the analysis and characterization of the protein component from the marine environment. Proteomic mass spectrometry is a high-throughput analysis of protein mixtures that does not require any prior knowledge of the original protein structures in the mixture, making it an ideal technique for marine studies. Potential marine applications of proteomics include: analyzing organisms cultured under different nutrient conditions to examine cellular expression and adaptation, profiling the marine dissolved and particulate organic matter pools to determine source information and understand long-term carbon preservation, and verifying genomic findings with proteomic analyses to determine which genes are translated and to what extent the protein is expressed. Although some major advances in marine studies and mass spectrometry have been made, there remains a significant amount of methods development and community education before the full potential of proteomics is reached.

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Section: Using Proteomics To Complement Genomic Findings In Marine Ecmentioning

confidence: 99%

Marine proteomics

Nunn¹,

Timperman²

2007

Mar. Ecol. Prog. Ser.

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“…The mass spectrometry analysis of in gel-digested proteins is not a quantitative method, and thus quantitative comparisons of different protein samples have to be done within the 2-D separation step. Multiple approaches are available: comparison of protein patterns on conventional 2-D gel electrophoresis followed by staining (Jung et al 2000; for discussion see Gygi et al 2000), Western blotting, or other immunoaffinity Rigaut et al 1999) and liquid-chromatography-based methods (Nilsson and Davidsson 2000). Relative quantification of proteins or peptides using mass spectrometry analyses is possible for samples labelled with a stable isotope such as deuterium and compared with a non-labelled sample (Gygi et al 2000).…”

Section: Proteomics -Analysing the Plant Proteomementioning

confidence: 99%

Plant functional genomics

Holtorf

Guitton

Reski

2002

Naturwissenschaften

114

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Functional genome analysis of plants has entered the high-throughput stage. The complete genome information from key species such as Arabidopsis thaliana and rice is now available and will further boost the application of a range of new technologies to functional plant gene analysis. To broadly assign functions to unknown genes, different fast and multiparallel approaches are currently used and developed. These new technologies are based on known methods but are adapted and improved to accommodate for comprehensive, large-scale gene analysis, i.e. such techniques are novel in the sense that their design allows researchers to analyse many genes at the same time and at an unprecedented pace. Such methods allow analysis of the different constituents of the cell that help to deduce gene function, namely the transcripts, proteins and metabolites. Similarly the phenotypic variations of entire mutant collections can now be analysed in a much faster and more efficient way than before. The different methodologies have developed to form their own fields within the functional genomics technological platform and are termed transcriptomics, proteomics, metabolomics and phenomics. Gene function, however, cannot solely be inferred by using only one such approach. Rather, it is only by bringing together all the information collected by different functional genomic tools that one will be able to unequivocally assign functions to unknown plant genes. This review focuses on current technical developments and their impact on the field of plant functional genomics. The lower plant Physcomitrella is introduced as a new model system for gene function analysis, owing to its high rate of homologous recombination.

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“…Unfortunately, 2-D PAGE also suffers from number of limitations in sensitivity and dynamic range of the staining procedures. Although significant improvements in the integration of 2-D PAGE into the automated MS analytical system have been achieved [37], alternative strategies for 2-D separations on both protein and peptide levels are also in development [38]. One of the first such systems employed size-exclusion liquid chromatography (SEC) followed by reversed-phase liquid chromatography (RPLC) to separate the mixture of proteins resulting from the lysis of Escherichia coli cells [39].…”

Section: Fraction Collection Couplingmentioning

confidence: 99%