Rapid verification of disulfide linkages in recombinant human growth hormone by tandem column tryptic mapping

Positive Effect of Acetylation on Proteomic Analysis Based on Liquid Chromatography with Atmospheric Pressure Chemical Ionization and Photoionization Mass Spectrometry

A typical bottom-up proteomic workflow comprises sample digestion with trypsin, separation of the hydrolysate using reversed-phase HPLC, and detection of peptides via electrospray ionization (ESI) tandem mass spectrometry. Despite the advantages and wide usage of protein identification and quantification, the procedure has limitations. Some domains or parts of the proteins may remain inadequately described due to inefficient detection of certain peptides. This study presents an alternative approach based on sample acetylation and mass spectrometry with atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI). These ionizations allowed for improved detection of acetylated peptides obtained via chymotrypsin or glutamyl peptidase I (Glu-C) digestion. APCI and APPI spectra of acetylated peptides often provided sequence information already at the full scan level, while fragmentation spectra of protonated molecules and sodium adducts were easy to interpret. As demonstrated for bovine serum albumin, acetylation improved proteomic analysis. Compared to ESI, gas-phase ionizations APCI and APPI made it possible to detect more peptides and provide better sequence coverages in most cases. Importantly, APCI and APPI detected many peptides which passed unnoticed in the ESI source. Therefore, analytical methods based on chymotrypsin or Glu-C digestion, acetylation, and APPI or APCI provide data complementary to classical bottom-up proteomics.

Utility of Atmospheric-Pressure Chemical Ionization and Photoionization Mass Spectrometry in Bottom-Up Proteomics

In a typical bottom-up proteomics workflow, proteins are enzymatically cleaved, and the resulting peptides are analyzed by HPLC with electrospray ionization (ESI) tandem mass spectrometry. This approach is practical and widely applied. It has, however, limitations mostly related to less efficient or even inefficient ionization of some peptides in ESI sources. Gas-phase ionization methods like atmospheric-pressure chemical ionization (APCI) or atmospheric-pressure photoionization (APPI) offer alternative ways of detecting various analytes. This work is a systematic study of the ionization efficiencies of peptides in ESI, APCI, and APPI and the applicability of the mentioned ionizations in proteomics. A set of peptide standards and bovine serum albumin digests were examined using a high-resolution mass spectrometer coupled to an ultra HPLC system. Since the ionization efficiency in APCI and APPI depends strongly on experimental conditions, the ion source settings and mobile phase compositions were optimized for each ionization technique. As expected, tryptic peptides were best detected using ESI. The numbers of chymotrypsin peptides successfully detected by ESI, APPI, and APCI were comparable. In the case of Glu-C digest, APPI detected the highest number of peptides. The results suggest that gas-phase ionization techniques, particularly APPI, are an interesting alternative for detecting peptides and delivering complementary data in proteomics.

Novel intein-based self-cleaving affinity tag for recombinant protein production in Escherichia coli

We evaluated several intein-based self-cleaving affinity tags for expression and single-step affinity chromatography purification of recombinant proteins produced in Escherichia coli. We used human growth hormone (hGH) as target protein that contains two internal disulfide bridges and an N-terminal phenylalanine. Use of N-terminal thiol-induced Sce VMA1 intein affinity tag resulted in purified hGH deficient in disulfide bonds. Inteins with self-cleavage inducible by pH and/or temperature shift were analyzed. N-terminal Ssp DnaX intein affinity tag resulted in a completely cleaved cytosolic protein, whereas N-terminal Ssp DnaB intein affinity tag resulted in a cytosolic fusion protein incapable of releasing hGH. Periplasmic expression of target protein was analyzed using an N-terminal signal peptide and C-terminal Ssp DnaX pH-inducible self-cleaving affinity tag. The fusion protein was properly expressed in pH 8 buffered culture medium. Fusion of a periplasmic signal peptide to the N-terminus of the POI allowed secretion to the periplasmic region and presence of the natural N-terminal amino acid of the POI following cleavage. Periplasmic expression of hGH fused to this novel C-terminal DnaX intein-based self-cleaving affinity tag made possible expression and purification of hGH protein containing disulfide bonds and free of extra amino acids.

High-throughput protein digestion by trypsin-immobilized monolithic silica with pipette-tip formula

Based on the monolithic silica gel materials with hierarchical pore structure and on the SPE devices (MonoTip) developed thereof, a trypsin-immobilized monolithic silica in a pipette tip (MonoTip Trypsin) suitable for digesting proteins has been newly developed. The surface of monolithic silica fixed into the tip was chemically modified with trypsin via an aminopropyl group. Trypsin-immobilized monolith successfully performed a rapid digestion of reduced and alkylated proteins with only a few times pipetting operation for the pre-treatment procedure of chromatographic analysis. The novel solid-phase digestion tool using monolithic silica allows a high-throughput trypsin proteolysis of bio-substances in proteomics.

Effects of modified digestion schemes on the identification of proteins from complex mixtures

In shotgun proteomics, a complex protein mixture is digested to peptides, separated, and identified by microcapillary liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). In this technology, complete protein digestion is often assumed. We show that, to the contrary, modifications to a standard digestion protocol demonstrate large, reproducible improvements in protein identification, a result consistent with digestion being a limiting factor in the efficiency of protein identification.

Proteolysis of whole cell extracts with immobilized enzyme columns as part of multidimensional chromatography

This paper describes the efficacy of immobilized trypsin columns in the digestion of cellular extracts that contained thousands of proteins. Effectiveness of proteolysis was evaluated with extracts of Escherichia coli by size-exclusion chromatography. Immobilized trypsin columns were operated in either the continuous-flow or stopped-flow mode at temperatures ranging from ambient to 37 degrees C with incubation times of 0-2 h. The results of these studies indicate that reduced and alkylated extracts of proteins from E. coli can be digested in 20 min when the enzyme column is operated at elevated temperature. The advantage of immobilized enzyme columns is that they can be easily incorporated into multidimensional separation systems for automated proteomics.

High-yield production of a human therapeutic protein in tobacco chloroplasts

Transgenic plants have become attractive systems for production of human therapeutic proteins because of the reduced risk of mammalian viral contaminants, the ability to do large scale-up at low cost, and the low maintenance requirements. Here we report a feasibility study for production of a human therapeutic protein through transplastomic transformation technology, which has the additional advantage of increased biological containment by apparent elimination of the transmission of transgenes through pollen. We show that chloroplasts can express a secretory protein, human somatotropin, in a soluble, biologically active, disulfide-bonded form. High concentrations of recombinant protein accumulation are observed (>7% total soluble protein), more than 300-fold higher than a similar gene expressed using a nuclear transgenic approach. The plastid-expressed somatotropin is nearly devoid of complex post-translational modifications, effectively increasing the amount of usable recombinant protein. We also describe approaches to obtain a somatotropin with a non-methionine N terminus, similar to the native human protein. The results indicate that chloroplasts are a highly efficient vehicle for the potential production of pharmaceutical proteins in plants.

Identification of the protein-drug adduct formed between aldehyde dehydrogenase and S-methyl-N,N-diethylthiocarbamoyl sulfoxide by on-line proteolytic digestion high performance liquid chromatography electrospray ionization mass spectrometry

Disulfiram has been used clinically as an aversion therapy treatment for recovering alcoholics. One of its metabolites, S-methyl-N, N-diethylthiocarbamoyl sulfoxide (MeDTC-SO), is currently believed by some to be the active metabolite in vivo. We demonstrate in this report that MeDTC-SO is a potent irreversible inhibitor of recombinant rat liver mitochondrial aldehyde dehydrogenase (rlmALDH), the enzyme responsible for oxidizing acetaldehyde formed during ethanol metabolism. Recombinant rlmALDH was inhibited by MeDTC-SO after in vitro incubation with an IC(50) = 4.62 microM. The inhibition of rlmALDH was found to be accompanied by a concomitant increase of approximately 100 Da to the molecular mass of the native enzyme as determined by on-line high performance liquid chromatography (HPLC) electrospray ionization mass spectrometry (LC/MS), indicating that a covalent modification has occurred. To determine the site and structure of this covalent adduct, we developed a novel approach to characterize specific protein-drug interactions by linking a proteolytic enzyme digestion cartridge on-line with LC/MS. The on-line pepsin digestion LC/MS of MeDTC-SO-inhibited rlmALDH revealed an ion at MH(2)(2+) = 500.9, which was not present in the pepsin digestion of the non-inhibited enzyme. This peptide was tentatively attributed to the putative active site peptide (FNQGQC(301)C(302)C(303)) plus the adduct. This peptide was subjected to analysis by LC/MS/MS, which allowed us to determine that the covalent modification was associated with a single carbamoyl adduct at Cys-302, which has been shown to be the active site nucleophile of the enzyme.

Capillary electrochromatography of peptides in a microfabricated system

Reversed-phase liquid chromatography of tryptic peptides is shown in the capillary electrochromatography mode using microfabricated columns. Although selectivity is different, a mixture of tryptic peptides from ovalbumin appears to be as easily separated in the CEC as HPLC mode. The major difference between a separation in the macrofabricated CEC column and conventional separations in the HPLC mode is that separations are more readily achieved in the isocratic mode in the lower surface area microfabricated CEC columns.