Monitoring the expression and purification of recombinant proteins by MALDI-TOF mass spectrometry

Emergence of whole-cell MALDI-MS biotyping for high-throughput bioanalysis of mammalian cells?

Since their inception in the 1970s, methods for classification of microorganisms based on mass spectral fingerprints obtained by MALDI-TOF MS have become a mainstay in environmental as well as in clinical microbiology. Recently, related whole-cell MALDI-TOF fingerprinting workflows have been adopted for the classification of mammalian cells. In this report we summarize this work and discuss the challenges of adapting whole-cell MS fingerprinting methods for the successful classification of mammalian cells. We highlight current limitations as well as opportunities and emerging applications of this technology in industrial and clinical settings, such as cell-line authentication, clinical diagnostics, and quality and productivity control in bioprocesses.

Functional Screening of Serine Protease Inhibitors in the Medical Leech Hirudo medicinalis Monitored by Intensity Fading MALDI-TOF MS

The blood-feeding invertebrates are a rich biological source of drugs and lead compounds to treat cardiovascular diseases because they have evolved highly efficient mechanisms to feed on their hosts by blocking blood coagulation. In this work, we focused our attention on the leech Hirudo medicinalis. We performed, by "intensity fading" MALDI-TOF mass spectrometry, a comprehensive detection and functional analysis of pre-existent peptides and small proteins with the capability of binding to trypsin-like proteases related to blood coagulation. Combining "intensity fading MS" and off-line LC prefractionation allowed us to detect more than 75 molecules present in the leech extract that interact specifically with a trypsin-like protease over a sample profile of nearly 2,000 different peptides/proteins in the 2-20-kDa range. Moreover we resolved 232 individual components from the complex mixture, 13 of which have high sequence homology with previously described serine protease inhibitors. Our findings indicate that such extracts are much more complex than expected. Additionally, intensity fading MS, when complemented with LC separation strategies, seems to be a useful tool to investigate complex biological samples, establishing a new bridge between profiling, functional peptidomics, and subsequent drug discovery.

A new method to purify hepatic CYP1A of Prochilodus scrofa, a Brazilian freshwater fish

Cytochromes P450 constitute a superfamily of the phase I enzymes whose primary task is the detoxification of both endogenous and xenobiotic compounds. Fish, among non-mammalian species, have received great interest because they are a direct food source for humans as well as conveyors of toxic chemicals to human beings. The aim of the present study was the purification of the hepatic isoform of CYP1A in Prochilodus scrofa (Prochilodontidae), a Brazilian fish, using only one chromatographic step. The purification of CYP1A was done by Reverse Phase HPLC on a C18 column. Purified CYP1A was characterized with respect to electrophoretic, immunochemical and biocatalyst properties. CYP1A fractions produced a single uniform band on SDS-PAGE with an apparent molecular mass of 58 kDa. Purified CYP1A of P. scrofa showed strong cross-reactivity with antibodies directed against CYP1A from trout. The fraction was also encapsulated in two different reconstituted systems; one composed of neutral lipids and another of negatively charged lipids. In both of them, we could detect EROD activity but not PROD activity, which confirms that the CYP1A was purified with all its enzyme activity. There was an increase of activity when CYP1A and NADPH cytochrome P450 (CYP) reductase were encapsulated in negatively charged lipids, which confirms that the charge of lipid is essential to CYP1A activity. All these characteristics strongly suggest that this new procedure is efficient for purifying hepatic CYP1A from P. scrofa, showing that the CYP1A isoform of this fish has a highly conserved protein region.

Quantitation of Underivatized Free Amino Acids in Mammalian Cell Culture Media Using Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

In this investigation, a quantitative matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) method was developed for the analysis of underivatized free amino acids in mammalian cell culture media. Calibration curves were developed for 12 amino acids over the linear range of 1-100 microM with coefficients of determination ranging from r2 = 0.9220 to r2 = 0.9973. An aerospray method was utilized for the sample deposition method, and the matrix, alpha-cyano-4-hydroxycinnamic acid, served as the internal standard. This assay was used to analyze bioreactor samples from five time points in the process. Concentrations determined through interpolation of the calibration curves were comparable to those obtained via reversed-phase HPLC based analysis with an average percent difference of 19.71%. Repeatability and intermediate precision studies were also performed, and the relative standard deviations ranged from 0.5943 to 21.41 and 3.157 to 18.97, respectively.

Identification of Protein Ligands in Complex Biological Samples Using Intensity-Fading MALDI-TOF Mass Spectrometry

The easy detection of biomolecular interactions in complex mixtures using a minimum amount of material is of prime interest in molecular and cellular biology research. In this work, a mass spectrometry MALDI-TOF based approach, which we call intensity-fading (IF MALDI-TOFMS), and which was designed for just such a purpose, is reported. This methodology is based on the use of the MALDI ion intensities to detect quickly the formation of complexes between nonimmobilized biomolecules in which a protein is one of the partners (protein-protein, protein-peptide, protein-organic molecule, and protein-nucleic acid complexes). The complex is detected through the decrease (fading) of the molecular ion intensities of the partners as directly compared to the MALDI mass spectrum of the mixture (problem and control molecules) following the addition of the target molecule. The potential of the approach is examined in several examples of model interactions, mainly involving small nonprotein and protein inhibitors of proteases, at both the qualitative and semiquantitative levels. Using this method, different protein ligands of proteolytic enzymes in total extracts of invertebrate organisms have been identified in a simple way. The proposed procedure should be easily applied to the high-throughput screening of biomolecules, opening a new experimental strategy in functional proteomics.

Practical quantitative biomedical applications of MALDI-TOF mass spectrometry

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) is used to obtain fast and accurate determinations of molecular mass, but quantitative determinations are generally made by other techniques. In this study we illustrate the practical utility of automated MALDI-TOFMS as a tool for quantifying a diverse array of biomolecules covering an extensive molecular weight range, and present in biological extracts and fluids. Growth hormone was measured in rat pituitary tissue; insulin in human pancreatic tissue; homovanillic acid in human urine; and LVV-hemorphin-7, epinephrine and norepinephrine in human adrenal and pheochromocytoma tissues. Internal standards including compounds of similar molecular weight, structural analogs or isotopomers were incorporated into each analysis. We report on the current practical limitations of quantitative MALDI-TOFMS and highlight some of the potential benefits of this technique as a quantitative tool.

In vivo labeling: a glimpse of the dynamic proteome and additional constraints for protein identification

Identities ascribed to the intact protein ions detected in MALDI-MS of whole bacterial cells or from other complex mixtures are often ambiguous. Isolation of candidate proteins can establish that they are of correct molecular mass and sufficiently abundant, but by itself is not definitive. An in vivo labeling strategy replacing methionine with selenomethionine has been employed to deliver an additional constraint for protein identification, i.e., number of methionine residues, derived from the shift in mass of labeled versus unlabeled proteins. By stressing a culture and simultaneously labeling, it was possible to specifically image the cells' response to the perturbation. Because labeled protein is only synthesized after application of the stress, it provides a means to view dynamic changes in the cellular proteome. These methods have been applied to identify a 15,879 Da protein ion from E. coli that was induced by an antibacterial agent with an unknown mechanism of action as SpY, a stress protein produced abundantly in spheroplasts. It has also allowed us to propose protein identities (and eliminate others from consideration) for many of the ions observed in MALDI (and ESI-MS) whole cell profiling at a specified growth condition.

Overexpression, purification, and characterization of glutaminase-interacting protein, a PDZ-domain protein from human brain

A human brain cDNA clone coding for a novel PDZ-domain protein of 124 amino acids has been previously isolated in our laboratory. The protein was termed GIP (glutaminase-interacting protein) because it interacts with the C-terminal region of the human brain glutaminase L. Here we report the heterologous expression of GIP as a histidine-tagged fusion protein in Escherichia coli cells. The induction conditions (temperature and isopropyl beta-d-thiogalactopyranoside concentrations) were optimized in such a way that GIP accounted for about 20% of the total E. coli protein. A simple and rapid procedure for purification was developed, which yielded 17 mg of purified GIP per liter of bacterial cell culture. The apparent molecular mass of the protein by SDS-PAGE was 16 kDa, whereas in native form it was determined to be 28 kDa, which suggests dimer formation. The nature and integrity of the recombinant protein were verified by mass spectrometry analysis. The functionality of the GIP protein was tested with an in vitro activity assay: after being pulled down with glutathione S-transferase-glutaminase, GIP was revealed by Western blot using anti-GIP antibodies. Furthermore, the glutaminase activity in crude rat liver extracts was inhibited by the presence of recombinant purified GIP protein.