Proteomics

Hoog, Carmen L. de; Mann, Matthias

doi:10.1146/annurev.genom.4.070802.110305

Cited by 193 publications

(147 citation statements)

References 120 publications

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“…Proteomics has had a major impact on the modern biosciences [25] and has decisively enhanced the field of basic and applied myology [26]. Proteomic profiling of muscle development, fiber differentiation, and muscle transformation has identified a large cohort of new potential markers of muscle biochemistry and their role in physiological adaptations to changed functional demands [27].…”

Section: Discussionmentioning

confidence: 99%

Mass spectrometric identification of dystrophin isoform Dp427 by on-membrane digestion of sarcolemma from skeletal muscle

Lewis

Ohlendieck

2010

Analytical Biochemistry

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a b s t r a c tAlthough the membrane cytoskeletal protein dystrophin of 427 kDa and its tightly associated glycoprotein complex are drastically affected in muscular dystrophy, recent large-scale proteomic investigations did not identify full-length dystrophin in muscle preparations and were unable to determine its molecular fate in dystrophinopathy. Because conventional two-dimensional gel electrophoresis underrepresents many low-abundance and membrane-associated protein species and in-gel trypsination is often hampered by an inefficient digestion of certain target proteins, here we have applied direct on-membrane digestion of one-dimensional blots of the sarcolemma-enriched fraction and the isolated dystrophinglycoprotein complex. This method succeeded in the mass spectrometric identification of dystrophin isoform Dp427 and associated glycoproteins as well as sarcolemmal dysferlin. In addition, protein bands representing established signature molecules of cross-contaminating membrane systems, such as the voltage-sensing dihydropyridine receptor of transverse tubules, the ryanodine receptor Ca 2+ -release channel of triad junctions, and the Ca 2+ -ATPase of the sarcoplasmic reticulum, were identified by mass spectrometry. Thus, proteomic approaches using on-membrane digestion might be suitable for future studies of low-abundance proteins, integral proteins, peripheral membrane proteins, and high-molecular-mass proteins. On-membrane digestion has the potential to develop into the method of choice for studying these classes of proteins, whose presence is otherwise missed by conventional gel electrophoresis-based proteomics.Ó 2010 Elsevier Inc. All rights reserved.The sarcolemma provides a crucial structural attachment site for the basement membrane at the outside of the muscle cell and for the membrane cytoskeleton on the inside of contractile fibers, strengthening the muscle periphery during contraction-relaxation cycles. The membrane cytoskeletal protein dystrophin and its tightly associated glycoprotein complex play a key role in the stabilization of the fiber surface by providing a linkage between the extracellular matrix component laminin and the cortical actin cytoskeleton [1][2][3]. Full-length dystrophin has a molecular mass of apparent 427 kDa and exhibits a complex domain structure. The membrane cytoskeletal element consists of an N-terminal actin-binding domain, a central spectrin-like rod domain with proline-rich hinge regions, a cysteine-rich domain, and a C-terminal region containing membrane-binding sites [4]. Although biochemical and cell biological studies have clearly shown that the primary genetic deficiency of dystrophin results in the drastic reduction of the dystrophin-associated glycoprotein complex in X-linked muscular dystrophy [5], recent large-scale proteomic studies have surprisingly not identified dystrophin isoform Dp427 in gel electrophoretically separated muscle preparations [6][7][8][9]. Mass spectrometric approaches also failed to identify integral dystrophin-associated glycoprote...

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Section: Discussionmentioning

confidence: 99%

Mass spectrometric identification of dystrophin isoform Dp427 by on-membrane digestion of sarcolemma from skeletal muscle

Lewis

Ohlendieck

2010

Analytical Biochemistry

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“…Proteomics, which aims at the systematic identification and quantification of all proteins in a biological system, has become a popular and effective analytical approach in life science research [1][2][3][4]. Over the past decade, thanks to the convergence of several important technological advances, MS-based proteomics technologies have progressed at a rapid pace and gained wide acceptance and usage.…”

Section: Introductionmentioning

confidence: 99%

Development and validation of a spectral library searching method for peptide identification from MS/MS

et al. 2007

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A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery of the same identifiable peptides by sequence database searching methods, which often are time-consuming and error-prone. A more precise and efficient method, in which previously observed and identified peptide MS/MS spectra are catalogued and condensed into searchable spectral libraries to allow new identifications by spectral matching, is seen as a promising alternative. To that end, an open-source, functionally complete, high-throughput and readily extensible MS/MS spectral searching tool, SpectraST, was developed. A high-quality spectral library was constructed by combining the high-confidence identifications of millions of spectra taken from various data repositories and searched using four sequence search engines. The resulting library consists of over 30 000 spectra for Saccharomyces cerevisiae. Using this library, SpectraST vastly outperforms the sequence search engine SEQUEST in terms of speed and the ability to discriminate good and bad hits. A unique advantage of SpectraST is its full integration into the popular Trans Proteomic Pipeline suite of software, which facilitates user adoption and provides important functionalities such as peptide and protein probability assignment, quantification, and data visualization. This method of spectral library searching is especially suited for targeted proteomics applications, offering superior performance to traditional sequence searching.

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“…Most often there is poor correlation between mRNA and protein expression. This is due to the fact that changes in the expression pattern at the mRNA level do not necessarily correlate with changes of the functional expression pattern at the protein level [2][3][4][5]. The word "proteome" describes the pool of proteins expressed in a cell or a tissue at a given time.…”

Section: Introductionmentioning

confidence: 99%

Recent advances in blood‐related proteomics

et al. 2005

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Service régional vaudois de transfusion sanguine, Lausanne, SwitzerlandBlood is divided in two compartments, namely, plasma and cells. The latter contain red blood cells, leukocytes, and platelets. From a descriptive medical discipline, hematology has evolved towards a pioneering discipline where molecular biology has permitted the development of prognostic and diagnostic indicators for disease. The recent advance in MS and protein separation now allows similar progress in the analysis of proteins. Proteomics offers great promise for the study of proteins in plasma/serum, indeed a number of proteomics databases for plasma/ serum have been established. This is a very complex body fluid containing lipids, carbohydrates, amino acids, vitamins, nucleic acids, hormones, and proteins. About 1500 different proteins have recently been identified, and a number of potential new markers of diseases have been characterized. Here, examples of the enormous promise of plasma/serum proteomic analysis for diagnostic/prognostic markers and information on disease mechanism are given. Within the blood are also a large number of different blood cell types that potentially hold similar information. Proteomics of red blood cells, until now, has not improved our knowledge of these cells, in contrast to the major progresses achieved while studying platelets and leukocytes. In the future, proteomics will change several aspects of hematology.

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Proteomics

Cited by 193 publications

References 120 publications

Mass spectrometric identification of dystrophin isoform Dp427 by on-membrane digestion of sarcolemma from skeletal muscle

Mass spectrometric identification of dystrophin isoform Dp427 by on-membrane digestion of sarcolemma from skeletal muscle

Development and validation of a spectral library searching method for peptide identification from MS/MS

Recent advances in blood‐related proteomics

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