Peptide fragments mass maps

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. 

The primary goal of peptide mapping is the verification of the amino acid sequence deduced from the genetic code of the recombinant protein. The protein backbone gets cleaved by typically two or three different endoproteinases like Lys-C, trypsin, and Glu-C to achieve maps with sequence-overlapping peptide fragments. These peptide mixtures can then be separated by LC or CE and analyzed on-line by MS to obtain sequence information. Often simple mass analysis matches the predicted primary sequence of the protein. However, sometimes mutations can lead to isobaric masses of peptides that can be overseen, if no further sequence analysis like N-terminal Edman sequencing and MS/MS is carried out. 

Applications of cze include the detection of trace amounts of DNA and the separation of peptide fragments. Furthermore, this technique is beneficial to forensic scientists because restriction mapping can be performed, allowing assays for DNA to be carried out at the scene of a crime (see Forensic testing). It is also possible to interface capillary electrophoresis on-line with a mass spectrometer as a sample introduction technique in the analysis of amino acids and proteins (70). Further improvements in capillary electrophoresis include the need to increase column capacity. Most reported separations involve the resolution of only 20—30 components, whereas high resolution hplc is capable of resolving several hundred components in a mixture (see Chromatography). 

Amino acid analysis and peptide mapping are standard methods in the course of protein identification processes [5, 6]. Molecular mass determination of whole molecules as well as peptide fragments with accuracies of about 0.01% by either matrix-assisted laser desorp-tion/ionization (MALDI)-MS for surface immobilized samples, or electrospray ionization (ESI)-MS for liquid samples, is another highly efficient protein identification method. These methods additionally support the identification of posttranslational modifications such as... 

Peptide-mass fingerprinting. In this approach, also known as peptide-mass mapping, the protein is first subjected to enzymatic digestion to generate a set of peptides that are unique to this protein (Section 8.4) [20,42-47]. The molecular mass of each fragment is determined accurately (within 0.5 Da) using MALDI-MS or ESI-MS. Correlation of these masses with the theoretical peptide... 

Peptide Mapping If the sequence of the protein is known, molecular mass determination of the peptide fragments in the unfractionated protein digest can rapidly identify the presence of phosphopeptides. Protein digest is analyzed by MALDI-MS (or ESI-MS), and phosphopeptides are recognized from the mass shift of 80 Da (or a multiple of 80 Da). 

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