Matrix-assisted laser desorption/ionization time-of-flight mass analysis of peptides

Specificity profiling of protein-binding domains using one-bead-one-compound Peptide libraries

One-bead-one-compound (OBOC) libraries consist of structurally related compounds (e.g., peptides) covalently attached to a solid support, with each resin bead carrying a unique compound. OBOC libraries of high structural diversity can be rapidly synthesized and screened without the need for any special equipment, and therefore can be employed in any chemical or biochemical laboratory. OBOC peptide libraries have been widely used to map the ligand specificity of proteins, to determine the substrate specificity of enzymes, and to develop inhibitors against macromolecular targets. They have proven particularly useful in profiling the binding specificity of protein modular domains (e.g., SH2 domains, BIR domains, and PDZ domains); subsequently, the specificity information can be used to predict the protein targets of these domains. The protocols outlined in this article describe the methodologies for synthesizing and screening OBOC peptide libraries against SH2 and PDZ domains, and the related data analysis. Curr. Protoc. Chem. Biol. 4:331-355 © 2012 by John Wiley & Sons, Inc.

Proteomic and scanning electron microscopic analysis of submandibular sialoliths

OBJECTIVES

Several theories have been proposed regarding the genesis of sialoliths, including the organic core theory, which suggests epithelial or bacterial etiology originating in the central core. Our aim was to use novel methodologies to analyze central areas (the core) of calculi from sialolithiasis patients.

MATERIALS AND METHODS

The structures of the halves of six submandibular salivary stones were analyzed by scanning electron microscopy (SEM). After structural analysis, from the other six halves, samples from the central parts of the core and peripheral parts of the core were digested with trypsin and analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The peptide mass fingerprints were compared with the results of in silico digestion.

RESULTS

SEM analysis of the sialoliths showed that organic structures (collagen/fibrous-like structures, bacterial fragments) were visible only outside of the core in the concentric layers of external areas, but not in the core area. The mass spectrometry (MS)/MS post-source decay experiments were completed from the four, most intense signals observed in the MS spectrum and human defensin was proven to be present in three of the examined samples, originated from the peripheral region of three cores.

CONCLUSIONS

Although proteomic analysis demonstrated defensin protein in the peripheral region of the core in three sialoliths, SEM failed to prove organic structures in the core.

CLINICAL RELEVANCE

New investigation modalities still cannot prove organic structures in the core, henceforward challenging the organic core theory.

Mass spectrometry-based identification of protein kinase substrates utilizing engineered kinases and thiophosphate labeling

Protein kinases constitute a large enzyme family with key roles in cellular signal transduction. One way to elucidate the functions of protein kinases is to systematically identify their downstream targets. We present here a simple and effective method to identify direct protein kinase substrates in native cell lysates. First, we isolate the activity of the kinase of interest by engineering the normal kinase to utilize bulky ATP analogs that cannot be used by normal cellular kinases. This allows specific labeling of substrates with thiophosphate tags by performing kinase reactions in cell lysates that also include bulky ATP-γ-S analogs. After digesting the proteins in the reaction mixture, thiophosphopeptides are isolated using a single-step capture-and-release protocol and identified by mass spectrometry. This technique is easy to use and generally applicable.

Tracking and quantification of 32P-labeled phosphopeptides in liquid chromatography matrix-assisted laser desorption/ionization mass spectrometry

Phosphoamino acid modifications on substrate proteins are critical components of protein kinase signaling pathways. Thus, diverse methodologies have been developed and applied to identify the sites of phosphorylated amino acids within proteins. Despite significant progress in the field, even the determination of phosphorylated residues in a given highly purified protein is not a matter of routine and can be difficult and time-consuming. Here we present a practicable approach that integrates into a liquid chromatography matrix-assisted laser desorption/ionization mass spectrometry (LC-MALDI MS) workflow and allows localization and quantification of phosphorylated peptides on the MALDI target plate prior to MS analysis. Tryptic digests of radiolabeled proteins are fractionated by reversed-phase LC directly onto disposable MALDI target plates, followed by autoradiographic imaging. Visualization of the radiolabel enables focused analysis of selected spots, thereby accelerating the process of phosphorylation site mapping by decreasing the number of spectra to be acquired. Moreover, absolute quantification of the phosphorylated peptides is permitted by the use of appropriate standards. Finally, the manual sample handling is minimal, and consequently the risk of adsorptive sample loss is very low. Application of the procedure allowed the targeted identification of six novel autophosphorylation sites of AMP-activated protein kinase (AMPK) and displayed additional unknown phosphorylated peptide species not amenable to detection by MS. Furthermore, autoradiography revealed topologically inhomogeneous distribution of phosphorylated peptides within individual spots. However, accurate analysis of defined areas within single spots suggests that, rather than such quantitative differences, mainly the manner of matrix crystallization significantly affects ionization of phosphopeptides.

Chapter 13. Characterizing proteolytic processing of chemokines by mass spectrometry, biochemistry, neo-epitope antibodies and functional assays

The nature, sequence, and length of the carboxy and amino termini of chemokines are important determinants of chemokine function, being essential for both efficient haptotactic gradient formation and cognate receptor activation events of these chemotactic cytokines. Chemokines are susceptible to proteolytic cleavage in both of these regions, which usually results in dramatic changes to the chemokine bioactivity. Herein we provide techniques to assess, detect, and characterize protease activity on chemokines and the biologic outcomes.

Letter: correlation between phosphorylation ratios by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis and enzyme kinetics

To identify the correlation between the phosphorylation ratios by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF MS) analysis and enzyme kinetics (Km, Vmax, and Vmax/Km) is important to understand whether MALDI-TOF MS can be applied for monitoring the properties of peptides that are substrates of protein kinases. The correlation between phosphorylation ratios and enzyme kinetics was examined using peptides for protein kinase C (PKC) and for 60 kDa phosphoprotein, encoded by the cellular sarcoma gene (c-Src). Phosphorylation ratios, analyzed by MALDI-ToF MS, showed higher correlation coefficient (r = or > +0.7) for Vmax/Km compared with that (r = or < -/+0.6) for Km or Vmax. For ion modes, a higher correlation coefficient between phosphorylation ratios and Vmax/Km was identified in the positive mode (r = or > +0.7) compared to that in the negative mode (r = or < +0.5). These results suggest that MALDI-ToF MS is a useful tool to evaluate Vmax/Km of peptides for protein kinases.

Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies

In recent years, several proteomic methodologies have been developed that now make it possible to identify, characterize, and comparatively quantify the relative level of expression of hundreds of proteins that are coexpressed in a given cell type or tissue, or that are found in biological fluids such as serum. These advances have resulted from the integration of diverse scientific disciplines including molecular and cellular biology, protein/peptide chemistry, bioinformatics, analytical and bioanalytical chemistry, and the use of instrumental and software tools such as multidimensional electrophoretic and chromatographic separations and mass spectrometry. In this unit, some of the common protein-profiling technologies are reviewed, along with the accompanying data-analysis tools.