Mass spectrometry characterization of the thermal decomposition/digestion (TDD) at cysteine in peptides and proteins in the condensed phase

Ultrafast protein digestion using an immobilized enzyme reactor following high-resolution mass spectrometry analysis for rapid identification of abrin toxin

Abrin toxin, highly dangerous with an estimated human lethal dose of 0.1-1 μg per kg body weight, has attracted much attention regarding criminal and terroristic misuse over the past decade. Therefore, developing a rapid detection method for abrin toxin is of great significance in the field of biosecurity. In this study, based on the specific dissociation method of an immobilized enzyme reactor, the trypsin immobilized reactor Fe3O4@CTS-GA-Try was prepared to replace free trypsin, and the immobilized enzyme digestion process was systematically investigated and optimized by using bovine serum albumin as the simulant of abrin. After 5 min one-step denaturation and reduction, a satisfactory peptide number and coverage were yielded with only 15 s assisted by an ultrasound probe to identify model proteins. Subsequently, abrin was rapidly digested using the established method, resulting in a stable and highly reproducible characteristic peptide number of 39, which can be analyzed by nanoelectrospray ionization coupled with high-resolution mass spectrometry. With the acquisition mode of full MS scan coupled with PRM, not only MS spectroscopy of total abrin peptides but also the corresponding MS/MS spectroscopy of specific abrin peptides can achieve the characteristic detection of abrin toxin and its different isoforms in less than 10 minutes, with high repeatability. This assay provides a universal platform and has great potential for the development of on-site detection and rapid mass spectrometric analysis techniques for macromolecular protein toxins and can further be applied to the integrated detection of chemical and biological agents.

Dry-heat-induced phosphoserine-specific fragmentation of ovalbumin

When subjected to dry-heating, egg white ovalbumin, a phosphoglycoprotein, undergoes fragmentation and forms soluble aggregates. We investigated the mechanisms of dry-heat-induced fragmentation of ovalbumin. SDS-PAGE analysis showed that ovalbumin fragmented into five polypeptides, and their amount increased over 6 h of dry-heat treatment at 120 °C. The fragments contained fewer or no phosphoserine, compared with that in crude ovalbumin. Liquid chromatography-tandem mass spectrometry analysis of tryptic digests revealed that the fragmentation sites were located on phosphoserine residues, S68 and S344. During fragmentation, the phosphoserine residues underwent conversion into dehydroalanine residues, which were subsequently hydrolyzed. The nitrogen from the dehydroalanine became a newly formed terminal amide group on the N-terminal fragment, while the remaining molecule predominantly formed a new terminal pyruvoyl group. Furthermore, the fragments were incorporated into monomers or soluble aggregates of ovalbumin via covalent and non-covalent bonds. This study demonstrated a novel mechanism for dry-heat-induced fragmentation of phosphoproteins.

Easy, Robust, and Repeatable Online Acid Cleavage of Proteins in Mobile Phase for Fast Quantitative LC-MS Bottom-Up Protein Analysis─Application for Ricin Detection

Sample preparation involving the cleavage of proteins into peptides is the first critical step for successful bottom-up proteomics and protein analyses. Time- and labor-intensiveness are among the bottlenecks of the commonly used methods for protein sample preparation. Here, we report a fast online method for postinjection acid cleavage of proteins directly in the mobile phase typically used for LC-MS analyses in proteomics. The chemical cleavage is achieved in 0.1% formic acid within 35 s in a capillary heated to 195 °C installed upstream of the analytical column, enabling the generated peptides to be separated. The peptides generated by the optimized method covered the entire sequence except for one amino acid of trastuzumab used for the method development. The qualitative results are extraordinarily stable, even over a long period of time. Moreover, the method is also suitable for accurate and repeatable quantification. The procedure requires only one manual step, significantly decreasing sample transfer losses. To demonstrate its practical utility, we tested the method for the fast detection of ricin. Ricin can be unambiguously identified from an injection of 10 ng, and the results can be obtained within 7-8 min after receiving a suspicious sample. Because no sophisticated accessories and no additional reagents are needed, the method can be seamlessly transferred to any laboratory for high-throughput proteomic workflows.

Proteins, possibly human, found in World War II concentration camp artifact

Museums displaying artifacts of the human struggle against oppression are often caught in their own internal struggle between presenting factual and unbiased descriptions of their collections, or relying on testament of survivors. Often this quandary is resolved in favor of what can be verified, not what is remembered. However, with improving instrumentation, methods and informatic approaches, science can help uncover evidence able to reconcile memory and facts. Following World War II, thousands of small, cement-like disks with numbers impressed on one side were found at concentration camps throughout Europe. Survivors claimed these disks were made of human cremains; museums erred on the side of caution—without documentation of the claims, was it justifiable to present them as fact? The ability to detect species relevant biological material in these disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained proteins, including collagens and hemoglobins, suggesting they were made, at least in part, of animal remains. A new protein/informatics approach to species identification showed that while human was not always identified as the top contributor, human was the most likely explanation for one disk. To our knowledge, this is the first demonstration of protein recovery from cremains. Data are available via ProteomeXchange with identifier PXD035267.

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.

Heat induced hydrolytic cleavage of the peptide bond in dietary peptides and proteins in food processing

We investigate the hypothesis that proteins and peptides are thermally degraded by hydrolytic bond cleavage of amide bonds, hence yielding shorter peptides as main degradation products. A series of fifteen pentapeptides with varying sequences was subjected to heating. Products were investigated by targeted UHPLC-ESI-tandem mass spectrometry and targeted analysis revealed formation of 2,5-diketopiperazines, di- and tri-peptides. Relative quantities of the thermal degradation were determined to show that hydrolytic cleavage is an important, however not dominant degradation pathway. A series of dietary intact proteins were subjected to heating and products formed analyzed by MALDI-TOF mass spectrometry. For the majority of proteins larger degradation products with m/z values between 900 and 2500 could be observed, which we tentatively assign as hydrolytic cleavage products. For coffee globulin a series of eleven short peptides formed through thermal hydrolytic cleavage could be unambiguously identified formed through thermal proteolysis. The identical products could as well be identified in samples of roasted coffee clearly illustrating the occurrence and relevance of thermally induced proteolysis of proteins.

Structural Analysis of the Effect of a Dual-FLAG Tag on Transthyretin

Recombinant proteins have increased our knowledge regarding the physiological role of proteins; however, affinity purification tags are often not cleaved prior to analysis, and their effects on protein structure, stability and assembly are often overlooked. In this study, the stabilizing effects of an N-terminus dual-FLAG (FT2) tag fusion to transthyretin (TTR), a construct used in previous studies, are investigated using native ion mobility-mass spectrometry (IM-MS). A combination of collision-induced unfolding and variable-temperature electrospray ionization is used to compare gas- and solution-phase stabilities of FT2-TTR to wild-type and C-terminal tagged TTR. Despite an increased stability of both gas- and solution-phase FT2-TTR, thermal degradation of FT2-TTR was observed at elevated temperatures, viz., backbone cleavage occurring between Lys9 and Cys10. This cleavage reaction is consistent with previously reported metalloprotease activity of TTR [Liz et al. 2009] and is suppressed by either metal chelation or excess zinc. This study brings to the fore the effect of affinity tag stabilization of TTR and emphasizes unprecedented detail afforded by native IM-MS to assess structural discrepancies of recombinant proteins from their wild-type counterparts.

Subcritical Water Hydrolysis of Peptides: Amino Acid Side-Chain Modifications

Previously we have shown that subcritical water may be used as an alternative to enzymatic digestion in the proteolysis of proteins for bottom-up proteomics. Subcritical water hydrolysis of proteins was shown to result in protein sequence coverages greater than or equal to that obtained following digestion with trypsin; however, the percentage of peptide spectral matches for the samples treated with trypsin were consistently greater than for those treated with subcritical water. This observation suggests that in addition to cleavage of the peptide bond, subcritical water treatment results in other hydrolysis products, possibly due to modifications of amino acid side chains. Here, a model peptide comprising all common amino acid residues (VQSIKCADFLHYMENPTWGR) and two further model peptides (VCFQYMDRGDR and VQSIKADFLHYENPTWGR) were treated with subcritical water with the aim of probing any induced amino acid side-chain modifications. The hydrolysis products were analyzed by direct infusion electrospray tandem mass spectrometry, either collision-induced dissociation or electron transfer dissociation, and liquid chromatography collision-induced dissociation tandem mass spectrometry. The results show preferential oxidation of cysteine to sulfinic and sulfonic acid, and oxidation of methionine. In the absence of cysteine and methionine, oxidation of tryptophan was observed. In addition, water loss from aspartic acid and C-terminal amidation were observed in harsher subcritical water conditions. Graphical Abstract ᅟ.

Transfer of Asymmetry between Proteinogenic Amino Acids under Harsh Conditions

The heating above 400 °C of serine, cysteine, selenocysteine and threonine leads to a complete decomposition of the amino acids and to the formation in low yields of alanine for the three formers and of 2-aminobutyric acid for the latter. At higher temperature, this amino acid is observed only when sublimable α-alkyl-α-amino acids are present, and with an enantiomeric excess dependent on several parameters. Enantiopure or enantioenriched Ser, Cys, Sel or Thr is not able to transmit its enantiomeric excess to the amino acid formed during its decomposition. The presence during the sublimation-decomposition of enantioenriched valine or isoleucine leads to the enantioenrichment of all sublimable amino acids independently of the presence of many decomposition products coming from the unstable derivative. All these studies give information on a potentially prebiotic key-reaction of abiotic transformations between α-amino acids and their evolution to homochirality.

Plasmonic Thermal Decomposition/Digestion of Proteins: A Rapid On-Surface Protein Digestion Technique for Mass Spectrometry Imaging

A method based on plasmon surface resonance absorption and heating was developed to perform a rapid on-surface protein thermal decomposition and digestion suitable for imaging mass spectrometry (MS) and/or profiling. This photothermal process or plasmonic thermal decomposition/digestion (plasmonic-TDD) method incorporates a continuous wave (CW) laser excitation and gold nanoparticles (Au-NPs) to induce known thermal decomposition reactions that cleave peptides and proteins specifically at the C-terminus of aspartic acid and at the N-terminus of cysteine. These thermal decomposition reactions are induced by heating a solid protein sample to temperatures between 200 and 270 °C for a short period of time (10-50 s per 200 μm segment) and are reagentless and solventless, and thus are devoid of sample product delocalization. In the plasmonic-TDD setup the sample is coated with Au-NPs and irradiated with 532 nm laser radiation to induce thermoplasmonic heating and bring about site-specific thermal decomposition on solid peptide/protein samples. In this manner the Au-NPs act as nanoheaters that result in a highly localized thermal decomposition and digestion of the protein sample that is independent of the absorption properties of the protein, making the method universally applicable to all types of proteinaceous samples (e.g., tissues or protein arrays). Several experimental variables were optimized to maximize product yield, and they include heating time, laser intensity, size of Au-NPs, and surface coverage of Au-NPs. Using optimized parameters, proof-of-principle experiments confirmed the ability of the plasmonic-TDD method to induce both C-cleavage and D-cleavage on several peptide standards and the protein lysozyme by detecting their thermal decomposition products with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The high spatial specificity of the plasmonic-TDD method was demonstrated by using a mask to digest designated sections of the sample surface with the heating laser and MALDI-MS imaging to map the resulting products. The solventless nature of the plasmonic-TDD method enabled the nonenzymatic on-surface digestion of proteins to proceed with undetectable delocalization of the resulting products from their precursor protein location. The advantages of this novel plasmonic-TDD method include short reaction times (<30 s/200 μm), compatibility with MALDI, universal sample compatibility, high spatial specificity, and localization of the digestion products. These advantages point to potential applications of this method for on-tissue protein digestion and MS-imaging/profiling for the identification of proteins, high-fidelity MS imaging of high molecular weight (>30 kDa) proteins, and the rapid analysis of formalin-fixed paraffin-embedded (FFPE) tissue samples.

Online Monitoring of Methanol Electro-Oxidation Reactions by Ambient Mass Spectrometry

Online detection of methanol electro-oxidation reaction products [e.g., formaldehyde (HCHO)] by mass spectrometry (MS) is challenging, owing to the high salt content and extreme pH of the electrolyte solution as well as the difficulty in ionizing the reaction products. Herein we present an online ambient mass spectrometric approach for analyzing HCHO generated from methanol electro-oxidation, taking the advantage of high salt tolerance of desorption electrospray ionization mass spectrometry (DESI-MS). It was found that HCHO can be detected as PhNHNH⁺=CH₂ (m/z 121) by DESI after online derivatization with PhNHNH₂. With this approach, the analysis of HCHO from methanol electro-oxidation by MS was carried out not only in acidic condition but also in alkaline media for the first time. Efficiencies of different electrodes for methanol oxidation at different pHs were also evaluated. Our results show that Au electrode produces more HCHO than Pt-based electrodes at alkaline pH, while the latter have higher yields at acidic solution. The presented methodology would be of great value for elucidating fuel cell reaction mechanisms and for screening ideal fuel cell electrode materials. Graphical Abstract ᅟ.

Biosynthesis and physicochemical characterization of a bacterial polysaccharide/polyamide blend, applied for microfluidics study in porous media

Screening among some new isolated bacteria from oily samples, which were capable of producing extracellular polymeric substances (EPSs), one was selected and identified as Bacillus sonorensis. An efficient micro-total analysis approach was carried out to assay the produced EPSs by this bacterium. Sucrose and yeast concentrations as carbon and nitrogen sources, respectively, sodium salt concentration and initial pH were selected to be the variables in experimental design. Production of EPS in optimal condition was increased by 5.3 times. Further EPS purification was carried out to identify the biopolymers. The bacteria produced high molecular weight biopolymers with a number average molecular weight (M̅n) of 9.1×10⁶g/mol determined by gel permeation chromatography (GPC). Biopolymer characterization demonstrated the biosynthesis of both polysaccharides and polyamides by the bacteria. For the biopolymer blend, thermal properties and morphological characteristics were studied using simultaneous differential scanning calorimetric and thermal gravimetric analyses (DSC/TGA) and field emission scanning electron microscope (FESEM) analyses. Finally, the biopolymer blend was injected into an oil saturated glass micro model to study the enhancement of oil recovery by biopolymer flooding in contrast with water flooding. It was found that oil recovery increased by 36%, from 23% using water flooding to 59% for biopolymer injection.

Enhancing Performance of Liquid Sample Desorption Electrospray Ionization Mass Spectrometry Using Trap and Capillary Columns

Desorption electrospray ionization mass spectrometry (DESI-MS) is a recent and important advance in the field that has extensive applications in surface analysis of solid samples but has also been extended to analysis of liquid samples. The liquid sample DESI typically employs a piece of fused silica capillary to transfer liquid sample for ionization. In this study, we present the improvement of liquid sample DESI-MS by replacing the sample transfer silica capillary with a trap column filled with chromatographic stationary phase materials (e.g., C4, C18). This type of trap column/liquid sample DESI can be used for trace analysis of organics and biomolecules such as proteins/peptides (in nM concentration) in high salt content matrices. Furthermore, when the sample transfer capillary is modified with enzyme covalently bound on its inside capillary wall, fast digestion (< 6 min) of proteins such as phosphoproteins can be achieved and the online digested proteins can be directly ionized using DESI with high sensitivity. The latter is ascribed to the freedom to select favorable spray solvent for the DESI analysis. Our data shows that liquid sample DESI-MS with a modified sample transfer capillary has significantly expanded its utility in bioanalysis.

Microfluidic Superheating for Peptide Sequence Elucidation

Herein, we introduce microfluidic superheating as a new method for peptide fragmentation prior to mass spectrometric analysis. The superheating conditions were found to be stable up to 240 °C for more than 30 min without elevated pressure or boiling of the aqueous sample. As proof of principle, we exposed the peptides ACTH1-10 and OVA257-264 to various superheating conditions, causing different degrees of decomposition. Optimized superheating conditions resulted in the entire peptide ladder sequence of the y-ions, allowing the amino acid sequence to be deduced from a single-stage mass spectrum. Thus, obtaining information in the same quality as from tandem mass spectrometry can be achieved by a single superheating step.

Characterization of the dehydration products due to thermal decomposition of peptides by liquid chromatography-tandem mass spectrometry

Thermal decomposition (TD) of proteins is being investigated as a rapid digestion step for bottom-up proteomics. Mass spectrometry (MS) analyses of the TD products of simple peptides and intact proteins have revealed several nonvolatile products at masses lower than the precursor biomolecule (M). In addition to products stemming from site-specific cleavages, many signals are also observed at a corresponding M-18, most likely because of dehydration (M-H2O) during the heating process. Understanding the structural nature of the water loss product is important in establishing the utility of their tandem mass spectra (collision-induced dissociation) in determining the precursor ion amino acid sequence in a bottom-up proteomic workflow. Dehydration of a peptide can take place from a variety of sources including side chain groups, C-terminus, and/or intramolecular cyclization (C to N-terminus cyclization). In this work, liquid chromatography-tandem MS (LC-MS/MS) and a series of standard peptides (angiotensin II, DRVYIHPF and its cyclic analog) are implemented to decipher the structure of the TD dehydration product. In addition, a derivatization strategy incorporating N-terminus acetylation was developed that allowed the direct comparison of tandem mass spectra of standard cyclic peptides with those resulting from the TD process, thus eliminating any ambiguity from the direct comparison of their mass spectra (due to gas-phase cyclization of b-ions, which can result in sequence scrambling of the precursor ion). Results from these investigations indicated that peptide dehydrated TD products were mostly linear in nature, and water loss was favored from the C-terminus carboxyl group or, when present, the aspartic acid side chain. Given the predictable nature of the formation of TD dehydration products, their MS/MS analysis can be of utility in providing complementary and confirmatory sequence information of the precursor peptide.

A ToF-MS with a highly efficient electrostatic ion guide for characterization of ionic liquid electrospray sources

We report on the development of a time-of-flight (ToF) mass spectrometer with a highly efficient electrostatic ion guide for enhancing detectability in ToF mass spectrometry. This 65-cm long ion guide consists of 13 cascaded stages of Einzel lens to collect a large fraction of emitted charges over a wide emission angle and energy spread for time-of-flight measurements. Simulations show that the ion guide can collect 100% of the charges with up to 23° emission half-angle or 30% energy spread irrespective of their specific charge. We demonstrate this ion guide as applied to electrospray ion sources. Experiments performed with tungsten needle electrospraying the ionic liquid EMI-BF4 showed that up to 80% of the emitted charges could be collected at the end of the flight tube. Flight times of monomers and dimers emitted from the needles were measured in both positive and negative emission polarities. The setup was also used to characterize the electrospray from microfabricated silicon capillary emitters and nearly 30% charges could be collected even from a 40(°) emission half-angle. This setup can thus increase the fraction of charge collection for ToF measurement and spray characteristics can be obtained from a very large fraction of the emission in real time.