Protein molecular mass

It should be pointed out that FAB, MALDI, and ESI can be used to provide ions for peptide mass maps or for microsequencing and that any kind of ion analyzer can support searches based only on molecular masses. Fragment or sequence ions are provided by instruments that can both select precursor ions and record their fragmentation. Such mass spectrometers include ion traps, Fourier transform ion cyclotron resonance, tandem quadrupole, tandem magnetic sector, several configurations of time-of-flight (TOF) analyzers, and hybrid systems such as quadrupole-TOF and ion trap-TOF analyzers. 

For analyses in the field, the ionization chamber will usually be connected to an automated module for sample collection and preparation. 

An algorithm has been developed to search databases for suites of protein masses automatically (Pineda et al.).65 In this case data from only one axis is being used, m/z values for the protonated molecular ions. Relative intensities are not used in the analysis. The algorithm also assesses the probability of accidental matches and false identifications. Significance testing allows a value to be assigned to each microorganism identification. 

In analyses where molecular masses are being matched, more accurate mass measurements provide more reliable matches and identifications.26,65,66 In a reference laboratory the mass accuracy to several decimal points, provided by a Fourier transform ion cyclotron resonance mass analyzer, may be desirable. In field or portable systems there is usually a trade-off in mass accuracy for size and ruggedness. Reliable identifications can be made with moderate mass accuracy, even 1 Da, if a large enough suite of molecular ions is recorded and used to search the database. If both positive ion and negative ion spectra are 

In another approach to improving the significance of mass matches, Demirev et al. have constructed a truncated database comprising proteins predicted to be abundant by estimating codon bias.72,73 The size of the entries for each organism can be selected, for example, as the 10 proteins predicted to be most abundant. 

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The selectivity of a gel, defined by the incremental increase in distribution coefficient for an incremental decrease in solute size, is related to the width of the pore size distribution of the gel. A narrow pore size distribution will typically have a separation range of one decade in solute size, which corresponds to roughly three decades in protein molecular mass (Hagel, 1988). However, the largest selectivity obtainable is the one where the solute of interest is either totally excluded (which is achieved when the solute size is of the same order as the pore size) or totally included (as for a very small solute) and the impurities differ more than a decade in size from the target solute. In this case, a gel of suitable pore size may be found and the separation carried out as a desalting step. This is very favorable from an operational point of view (see later). 

Protein Molecular Mass (kD) Content (wt 7c) Localization Function... 

As is the case with identifications based on protein molecular masses, it appears that the use of tryptic or other peptide masses as the basis for identification is extended with difficulty to mixtures of microorganisms. This reflects unpredictable suppression. Another limitation is redundancy of peptide masses across several microorganisms. For example, the most abundant proteins (SASPs), and thus the most abundant peptides, in spores of Bacillus anthracis and the closely related pesticide Bacillus thuringiensis have extensive sequence homology.25,82... 

Protein Molecular mass (kDa) Protein Molecular mass (kDa) Protein Molecular mass (kDa)... 

Size-based analysis of SDS-protein complexes in polyacrylamide gels (SDS-PAGE) is the most common type of slab gel electrophoresis for the characterization of polypeptides, and SDS-PAGE is one of the most commonly used methods for the determination of protein molecular masses.117 The uses for size-based techniques include purity determination, molecular size estimation, and identification of posttranslational modifications.118119 Some native protein studies also benefit from size-based separation, e.g., detection of physically interacting oligomers. 

G. Protein molecular mass from electrospray. The enzyme lysozyme33 exhibits MHJ[+ peaks at mlz = 1 789.1, 1 590.4, 1 431.5, 1 301.5, and 1 193.1. Follow the procedure of Table 22-3 to find the mean molecular mass and its standard deviation. 

Figure 26-38 Calibration curve for protein molecular mass in sodium dodecyl sulfate-capillary gel electrophoresis. The abscissa, fre, Is the migration time of each protein divided by the migration time of a small dye molecule. [Data from j. K, Grady, J. Zang, t. M. Laue, RArosio, and N. D, Chasteen, "Characterization of the H- and L-Subunlt Ratios in Ferritins by Sodium Dodecyl Sulfate-Capillary Gel Electrophoresis," Anal. Biochem. 2002,302.263.)...

The product of the crystal density and the unit-cell volume (determined from crystallographic analysis, Chapter 4) gives the total mass within the unit cell. This quantity, expressed in daltons, is the sum of all atomic masses in one unit cell. If the protein molecular mass and the number of protein molecules per unit cell are known, then the remainder of the cell can be assumed to be water, thus establishing the proteinlwater ratio. 

Fig. 4. SDS-PAGE analysis of BglA treated with N-glycosidase F. Lane S, protein molecular mass standards lane 1, purified secreted BglA (2.4 pg) lane 2, purified secreted BglA (2.4 pg) treated with N-glycosidase F.

TABLE I Fundamental Properties of Amino Acid Residues in Terms of Occurrence in Proteins, Molecular Mass, Molecule Volume, Accessible Surface Area, Partial Specific Volume, pKa of Ionizing Side Chains, and Relative Hydrophobicity... 

Protein (molecular mass Plant source (family) Target (other targets)... 

Protein (molecular mass number of cysteines other properties) Plant source (family) (plant part) Target (other targets) / in vivo effects ... 

The protein molecular mass is insufficient information for identification, but it is adequate to confirm identity therefore, MS is one of the preferred techniques for characterization and quality control of recombinant proteins and other biomolecules. In the same way, it has been used to study posttranslational modifications (like glycosylation and disulfide bonding pattern), and other processes that can modify protein mass.11... 

A second approach exploits the information contained in genome and protein sequencing databases. The masses of a set of proteins from the bacterial strain under study are determined and used to search databases for protein molecular mass matching. This has been used as a method to differentiate B. subtilis and E. coli, two organisms that have completely sequenced genomes.34... 

SDS Gel Band Protein Molecular Mass (kDa) Monomer Molecules/ Cell, Thousands Oligomeric State Approximate Proportion, % Peripheral or Integral Chromosome Location Associated Diseases ... 

Soluble yeast protein was calculated based on 1 mg of yeast protein being derived from harvesting 6 X lo cells. Calculations are based on a protein molecular mass of 50 kDa and 100% efficiencies of the procedures used. 

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