Protein mass mapping

FIGURE 13.5 The total ion chromatogram and deconvoluted protein mass map for a ID LC/MS analysis of yeast ribosomal proteins. The bubble size is proportional to component intensity. 

Bark SJ, Muster N, Yates JR, Siuzdak G (2001) High temperature protein mass mapping using a thermophilic protease. J Am Chem Soc 123 1774-1775... 

B.J. Zeskind, C.D. Jordan, W. Timp, L. Trapani, G. Waller, V. Horodincu, D.J. Ehrlich, P. Matsudaira, Nucleic acid and protein mass mapping by live-cell deep-ultraviolet microscopy. Nat. Methods 4, 567-568 (2007)... 

Matrix-associated laser desorption ionization with a time-of-flight mass analyser (MALDl-ToF) was used to examine the crude tryptic peptide mixture from a number of the proteins, without HPLC separation, to provide a mass map, i.e. a survey of the molecular weights of the peptides generated by the digestion process. 

Protein expression mapping by 2D gel electrophoresis and mass spectrometry... 

The use of 2D gel electrophoresis and mass spectrometry to identify proteins was discussed in Chapter 2. Protein expression mapping involves the use of these methodologies to compare expression patterns in different cell types or in the same cell type that has been exposed to different... 

The utility of protein expression mapping using 2D gel electrophoresis and mass spectrometry has been demonstrated for several experimental systems. One application has been to assess the differences in protein expression between normal and cancerous cells. For example, expression mapping has been used to identify protein markers for bladder cancer (Ostergaard et al., 1999). This was accomplished by identifying proteins released into the urine of patients with and without bladder cancer using 2D electrophoresis and mass spectrometry. 

Figure 3.1. Protein expression mapping using 2-D electrophoresis and mass spectrometry. The purpose is to compare protein expression patterns between cell types or in the same cell type under different growth conditions. Proteins are extracted from the different cell types and separated by 2D gel electrophoresis. Image analysis programs are used to compare the spot intensities between gels and identify proteins that are differentially expressed. The protein of interest is excised from the gel and its identity is determined by mass spectrometry. The power of the method increases greatly if the identity of a large number of proteins on the gel is known and present in a database because information can then be obtained without further mass spectrometry.

Use of mass spectrometry for protein-protein interaction mapping... 

The difficulty with protein arrays is that proteins do not behave as uniformly as nucleic acid. Protein function is dependent on a precise, and fragile, three-dimensional structure that may be difficult to maintain in an array format. In addition, the strength and stability of interactions between proteins are not nearly as standardized as nucleic acid hybridization. Each protein-protein interaction is unique and could assume a wide range of affinities. Currently, protein expression mapping is performed almost exclusively by two-dimensional electrophoresis and mass spectrometry. The development of protein arrays, however, could provide another powerful... 

The experiments described above indicate that technology is available to couple SPR with mass spectrometry. These methods should be useful for protein-protein interaction mapping. For example, immobilized proteins can be used as hooks for fishing binding partners from complex protein mixtures under native conditions. The coupling of techniques can lead not only to the rapid identification of interacting proteins but will also provide information on the kinetic parameters of the interaction. This approach should serve as an excellent complement to the use of in vivo techniques such as the yeast two-hybrid system. 

D Liquid Mass Mapping of Tumor Cell Line Secreted Samples, Application to Metastasis-Associated Protein Profiles... 

A 2D liquid mass mapping method has been developed in our laboratory for the analytical profiling of proteins in complex biological material. In the present study, we demonstrate the capability of this method for comparative protein mapping of isogenic... 

FIGURE 10.7 Annotated mass maps of MCF10A, CAla, and CAld. Normalized maps show identities and intensities of proteins from 3 MCF10 cell lines at pH 5.6-6.0 and 7.6-8.0. 

Kreunin, P, Urquidi, V., Luhman, D. M., Goodison, S. (2004). Identification of metastasis-associated proteins in a human tumor metastasis model using the mass-mapping technique. Proteomics 4(9), 2754—2765. 

The ProteinChip System from Ciphergen Biosystems uses patented SELDI (Surface-Enhanced Laser Desorption/Ionization) ProteinChip technology to rapidly perform the separation, detection, and analysis of proteins at the femtomole level directly from biological samples. ProteinChip Systems use ProteinChip Arrays which contain chemically (cationic, anionic, hydrophobic, hydrophilic, etc.) or biochemically (antibody, receptor, DNA, etc.) treated surfaces for specific interaction with proteins of interest. Selected washes create on-chip, high-resolution protein maps. This protein mass profile, or reten-tate map of the proteins bound to each of the ProteinChip Array surfaces, is quantitatively detected in minutes by the ProteinChip Reader. 

Proteomics of Protein Binders Peptide Mass Mapping Using Mass Spectrometry... 

This procedure is called Peptide Mass Mapping (PMM), which is defined as a means of protein identification by comparing observed masses (m/z values) with predicted masses of digested proteins contained in a database. 

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