Polypeptide sequencing by liquid chromatography mass spectrometry

Origins, Technological Advancement, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.

Origins, Technological Development, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.

Micro LC/MS in drug analysis and metabolism studies

LC/MS has become a routine research tool in some laboratories. Although no single approach to LC/MS presently is without limitations, each approach offers encouraging results and prompts continued improvements. The remaining hurdles appear to be the introduction of total LC effluent into the MS, increased sensitivity, and the ability to analyze higher molecular weight, polar molecules. The micro LC/MS results discussed in this paper offer an opportunity for significantly increased sensitivity by allowing total micro LC effluent introduction into the MS. It remains to be seen whether the development of micro LC column and equipment technology will allow practical micro LC/MS. It may someday provide improved separation of drugs, metabolites, and their conjugates from high levels of endogenous materials in reasonable time periods. Currently, the impressive efficiencies demonstrated for micro LC columns involve mixtures containing low molecular weight solutes that are perhaps more amenable to GC analysis. The analyst routinely involved with problem solving must deal with complex mixtures composed of components with large concentration differences. The future of micro LC, and hence micro LC/MS, will depend upon how well the technique helps solve problems. We believe the future is bright for micro LC/MS. The techniques may require some fine tuning of operating procedures, just as with capillary GC/MS, but certainly the potential for increased efficiency and sensitivity is worth the effort. Currently we are testing a new micro LC/MS DLI probe wherein the exit of the micro column is within 1 cm of the MS ion source [82]. The micro LC column is contained within the DLI probe and should offer the lowest dead volume and the least extracolumn effects yet achieved by LC/MS. Initial testing of this new probe is under way, and experimental results will be reported subsequently. The analytical potential of micro LC/MS is receiving considerable interest. Practical micro LC performance can provide increased capabilities to all types of LC/MS reported to date, and perhaps offer new insight into alternative methods of LC/MS not yet reported. We look forward to learning of these breakthroughs as they become available.

Combined high performance liquid chromatography mass spectrometry

Combined gas chromatography mass spectrometry, because of its ability to provide both high sensitivity and specificity, has become a vital technique for the identification and quantitation of natural and synthetic chemicals in a wide variety of areas. Unfortunately, a very large number of organic compounds are not directly amenable to gas chromatography since they are thermally labile and/or of low volatility. Chemical modification of compounds of interest can assist in some cases, but it is not universally applicable. High performance liquid chromatography has been increasingly utilized for studies of compounds of these types since heat is not usually involved in the analysis. Combined liquid chromatography mass spectrometry would lend a new dimension to these studies, enabling the separating ability of the liquid chromatograph to be combined with the sensitivity and specificity of the mass spectrometer. Approaches to liquid chromatography mass spectrometry are discussed. Using examples from our liquid chromatographic mass spectrometric studies of natural compounds, drugs and pesticides, the current abilities of such systems to identify and quantify natural and synthetic chemicals present in a complex matrix of other chemicals are described.

Sequencing of peptide mixtures by Edman degradation and field-desorption mass spectrometry

A new procedure is described for sequencing of peptide mixtures by a combination of Edman degradation and field-desorption mass spectrometry. The procedure involves measurement of the mass values of quasi-molecular ions ([M + H]+) of constituent peptides in the mixture and their fragments degraded by the Edman method. Calculation of all the possible mass differences of the mass values before and after degradation and identification of the phenylthiohydantoins released reveal the N-terminal amino acids of individual peptides in the mixture. Repetition of these operations gives the amino acid sequences of individual peptides in the mixture. As typical examples, the sequencing of peptide mixtures prepared by proteolytic digestion of glucagon are described. In addition, a computer program was designed for determining the possible sequences of proteins from the partial sequences and mass values of their proteolytic peptides. Output data showed that the entire amino acid sequence of glucagon can be determined by only four and two cycles of degradation of chymotryptic and tryptic peptides, respectively.

Use of variable p(H) interface to a mass spectrometer for the measurement of dissolved volatile compounds

A wide variety of dissolved chemicals can be measured continuously with some specificity by directly interfacing a relatively inexpensive mass spectrometer to a solution. Specifically, we describe the construction and initial use of a membrane interace to a mass spectrometer which allows the continuous measurement of the concentration of dissolved volatile compounds in buffered aqueous solution. In addition to volatile compounds that do not dissociate appreciably at p(H) 7 (e.g., ethanol, ethylene glycol), volatile acids and bases, such as acetic acid or ammonia, can be measured with the interface is operated within the range 1</=p(H)</=12. We also discuss the sensitivity of the system to variations in flow rate and describe a satisfactory method for providing sufficiently constant flow rates.