Post-source Decay Research Articles

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses.

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.

Surface assisted laser desorption/ionization mass spectrometry of lithium cationized lignans – A tool for rapid screening of plant extracts

Lignans are one of the most widespread classes of plant secondary metabolites possessing unique biological activities. The search for new sources of such compounds, their screening and identification in plant biomass is an urgent task, requiring the use of advanced analytical methods. In the present study, matrix-free surface assisted laser desorption/ionization (SALDI) mass spectrometry was proposed for its solution. The combination of carbon nanocoating sputtered on a target plate with lithium cationization allowed obtaining high-quality mass spectra of eight coniferous wood lignans with different bonds between aromatic units (secoisolariciresinol, matairesinol, 7-hydroxymatairesinol, nortrachelogenin, pinoresinol, guaiacylglycerol-β-guaiacyl ether, dehydrodihydrodiisoeugenol, and divanillin). Three types of fragmentation methods (post-source decay, high- and low-energy collision induced dissociation) for the first time were implemented on two types of MALDI instruments. Regardless of tandem mass spectrometry technique, lignans demonstrated the similar fragmentation patterns including the cleavage of bonds between aromatic units with the formation of mostly lithiated product ions. The low-energy collision induced dissociation in quadrupole ion trap provided the most informative tandem mass spectra and multi-stage fragmentation capabilities in structural studies. On this basis, an approach to rapid, high-throughput, and low-cost screening and tentative identification of lignans including isomeric compounds in plant biomass was developed and successfully tested on real samples of pine, fir, spruce, and larch knotwood extracts.

Lipidomic Profile of Human Sperm Membrane Identifies a Clustering of Lipids Associated with Semen Quality and Function.

Reduced sperm motility and/or count are among the major causes of reduced fertility in men, and sperm membranes play an important role in the spermatogenesis and fertilization processes. However, the impact of sperm lipid composition on male fertility remains under-investigated. The aim of the present study was to perform a lipidomic analysis of human sperm membranes: we performed an untargeted analysis of membrane lipid composition in fertile (N = 33) and infertile subjects (N = 29). In parallel, we evaluated their serum lipid levels. Twenty-one lipids were identified by their mass/charge ratio and post-source decay spectra. Sulfogalactosylglycerolipid (SGG, seminolipid) was the most abundant lipid component in the membranes. In addition, we observed a significant proportion of PUFAs. Important differences have emerged between the fertile and infertile groups, leading to the identification of a lipid cluster that was associated with semen parameters. Among these, cholesterol sulfate, SGG, and PUFAs represented the most important predictors of semen quality. No association was found between the serum and sperm lipids. Dietary PUFAs and SGG have acknowledged antioxidant functions and could, therefore, represent sensitive markers of sperm quality and testicular function. Altogether, these results underline the important role of sperm membrane lipids, which act independently of serum lipids levels and may rather represent an independent marker of reproductive function.

Unusual modifications of protein biomarkers expressed by plasmid, prophage, and bacterial host of pathogenic Escherichia coli identified using top‐down proteomic analysis

RationalePathogenic bacteria often carry prophage (bacterial viruses) and plasmids (small circular pieces of DNA) that may harbor toxin, antibacterial, and antibiotic resistance genes. Proteomic characterization of pathogenic bacteria should include the identification of host proteins and proteins produced by prophage and plasmid genomes.MethodsProtein biomarkers of two strains of Shiga toxin–producing Escherichia coli (STEC) were identified using antibiotic induction, matrix‐assisted laser desorption/ionization tandem time‐of‐flight (MALDI‐TOF‐TOF) tandem mass spectrometry (MS/MS) with post‐source decay (PSD), top‐down proteomic (TDP) analysis, and plasmid sequencing. Alphafold2 was also used to compare predicted in silico structures of the identified proteins to prominent fragment ions generated using MS/MS‐PSD. Strain samples were also analyzed with and without chemical reduction treatment to detect the attachment of pendant groups bound by thioester or disulfide bonds.ResultsShiga toxin was detected and/or identified in both STEC strains. For the first time, we also identified the osmotically inducible protein (OsmY) whose sequence unexpectedly had two forms: a full and a truncated sequence. The truncated OsmY terminates in the middle of an α‐helix as determined by Alphafold2. A plasmid‐encoded colicin immunity protein was also identified with and without attachment of an unidentified cysteine‐bound pendant group (~307 Da). Plasmid sequencing confirmed top‐down analysis and the identification of a promoter upstream of the immunity gene that is activated by antibiotic induction, that is, SOS box.ConclusionsTDP analysis, coupled with other techniques (e.g., antibiotic induction, chemical reduction, plasmid sequencing, and in silico protein modeling), is a powerful tool to identify proteins (and their modifications), including prophage‐ and plasmid‐encoded proteins, produced by pathogenic microorganisms.

MALDImID: Spatialomics R package and Shiny app for more specific identification of MALDI imaging proteolytic peaks using LC-MS/MS-based proteomic biomarker discovery data.

Matrix-assisted laser desorption/ionization (MALDI) imaging of proteolytic peptides from formalin-fixed paraffin embedded (FFPE) tissue sections could be integrated in the portfolio of molecular pathologists for protein localization and tissue classification. However, protein identification can be very tedious using MALDI-time-of-flight (TOF) and post-source decay (PSD)-based fragmentation. Hereby, we implemented an R package and Shiny app to exploit liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic biomarker discovery data for more specific identification of peaks observed in bottom-up MALDI imaging data. The package is made available under the GPL 3 license. The Shiny app can directly be used at the following address: https://biosciences.shinyapps.io/Maldimid.

Top-down proteomic identification of protein biomarkers of Xylella fastidiosa subsp. fastidiosa using MALDI-TOF-TOF-MS and MS/MS

Protein biomarkers were identified from bacterial cell lysates of two sequenced strains of Xylella fastidiosa subsp. fastidiosa (Xff), the causal agent of Pierce's Disease of grapevine, using MALDI-TOF-TOF tandem mass spectrometry (MS/MS) and top-down proteomic analysis. Proteins were identified from their intact masses as well as sequence-specific fragment ions resulting from the aspartic acid effect detected by MS/MS and post-source decay (PSD). Two Xff strains from California were studied, M23 isolated from almond in Kern County and Stag's Leap isolated from grapevine in Napa County. The two strains are pathogenically identical or highly similar. Most of the proteins identified were highly conserved, e.g., 10 kDa chaperonin, cold-shock and/or DNA-binding, ribosomal and hypothetical proteins. The amino acid sequences and post translational modifications (PTM) of these conserved proteins were identical between the two Xff strains. However, the amino acid sequence of an outer membrane/hypothetical protein differed significantly between the two strains and could be a useful biomarker to distinguish between these closely related strains. In silico signal peptide analysis suggest that the outer membrane/hypothetical protein are secreted lipoproteins (SPII) with a putative prosthetic group attached to the only cysteine residue (C19) before or after removal of an 18-residue N-terminal signal peptide. However, only y-type fragment ions were detected by MS/MS-PSD which precluded confirmation of the site of sequence truncation and/or attached PTM. The annotated genomes of the two strains indicate ten to twenty proteins that are either lipoproteins or are associated with assembly, modification, or transport of lipoproteins. In consequence, a variety of prosthetic groups, e.g. diacylglycerol, may be attached to C19 in the mature protein.

Toxin and phage production from pathogenic E. coli by antibiotic induction analyzed by chemical reduction, MALDI-TOF-TOF mass spectrometry and top-down proteomic analysis.

Shiga toxin-producing Escherichia coli (STEC) are an on-going threat to public health and agriculture. Our laboratory has developed a rapid method for identification of Shiga toxin (Stx), bacteriophage and host proteins produced from STEC. We demonstrate this technique on two genomically sequenced STEC O145:H28 strains linked to two major outbreaks of foodborne illness occurring in 2007 (Belgium) and 2010 (Arizona). Our approach is to induce expression of stx, prophage and host genes by antibiotic exposure, chemically reduce samples and identify protein biomarkers from unfractionated samples using MALDI-TOF-TOF, tandem mass spectrometry (MS/MS) and post-source decay (PSD). The protein mass and prominent fragment ions were used to identify protein sequences using top-down proteomic software developed in-house. Prominent fragment ions are the result of polypeptide backbone cleavage (PBC) resulting from the aspartic acid effect fragmentation mechanism. The B-subunit of Stx and acid-stress proteins HdeA and HdeB were identified in both STEC strains in their intramolecular disulfide bond-intact and reduced states. In addition, two cysteine-containing phage tail proteins were detected and identified from the Arizona strain but only under reducing conditions which suggests that bacteriophage complexes are bound by intermolecular disulfide bonds. An acyl carrier protein (ACP) and a phosphocarrier protein (HPr) were also identified from the Belgium strain. ACP was post-translationally modified with attachment of a phosphopantetheine linker at residue S36. The abundance of ACP (plus linker) was significantly increased upon chemical reduction suggesting the release of fatty acids bound to the ACP + linker at a thioester bond. MS/MS-PSD revealed dissociative loss of the linker from the precursor ion as well as fragment ions with and without the attached linker consistent with its attachment at S36. This study demonstrates the advantages of chemical reduction in facilitating the detection and top-down identification of protein biomarkers of pathogenic bacteria.

BOA/DHB/Na: An Efficient UV-MALDI Matrix for High-Sensitivity and Auto-Tagging Glycomics.

Matrix selection is a critical factor for success in glycomics studies using matrix-assisted laser desorption/ionization–mass spectrometry (MALDI–MS). In this study, we evaluated and optimized a new solid ionic matrix—O-benzylhydroxylamine (BOA)/2,5-dihydroxybenzoic acid (DHB)/Na—containing BOA and a small amount of sodium as the counter salt of DHB. The concentration of a mixture of BOA/DHB/Na and glycans on a MALDI target plate led to O-benzyloxy tagging of the reducing ends of the glycans. The BOA/DHB/Na matrix showed excellent aggregation performance and the ability to form a homogeneous solid salt on the MALDI target plate with a water-repellent surface. In addition, the BOA/DHB/Na matrix showed a simple peak pattern with suppressed in-source and post-source decay of the reducing ends of the glycans, as well as improved ionization efficiency of glycans. Utilizing the characteristics of the BOA/DHB/Na matrix, O-glycan analysis of porcine stomach mucin showed excellent detection sensitivity and reproducibility of the peak patterns. This BOA/DHB/Na matrix can accelerate glycomics studies using MALDI–MS and, in combination with other organic salt-type matrices that we have developed, constitutes a valuable tool for glycomics studies.

Top-down proteomic identification of plasmid and host proteins produced by pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry.

Fourteen proteins produced by three pathogenic Escherichia coli strains were identified using antibiotic induction, MALDI-TOF-TOF tandem mass spectrometry (MS/MS) and top-down proteomic analysis using software developed in-house. Host proteins as well as plasmid proteins were identified. Mature, intact protein ions were fragmented by post-source decay (PSD), and prominent fragment ions resulted from the aspartic acid effect fragmentation mechanism wherein polypeptide backbone cleavage (PBC) occurs on the C-terminal side of aspartic acid (D), glutamic acid (E) and asparagine (N) residues. These highly specific MS/MS-PSD fragment ions were compared to b- and y-type fragment ions on the C-terminal side of D-, E- and N-residues of in silico protein sequences derived from whole genome sequencing. Nine proteins were found to be post-translationally modified with either removal of an N-terminal methionine or a signal peptide. The protein sequence truncation algorithm of our software correctly identified all full and truncated protein sequences. Truncated sequences were compared to those predicted by SignalP. Nearly complete concurrence was obtained except for one protein where SignalP mis-identified the cleavage site by one residue. Two proteins had intramolecular disulfide bonds that were inferred by the absence of PBC on the C-terminal side of a D-residue located within the disulfide loop. These results demonstrate the utility of MALDI-TOF-TOF for identification of full and truncated bacterial proteins.

Sequestration of the ionizing proton in singly charged metastable protein ions generated by MALDI

A hypothesis is proposed for the preferential ionization/protonation of arginine residues in metastable protein ions. This phenomenon has significant consequences for detection of protein fragments resulting from polypeptide backbone cleavage. Preferential ionization at arginine (when present) is based upon MS/MS analysis of singly charged/protonated metastable protein ions: YahO, CspC, CspE, B-subunit of Shiga toxin 2 and thioredoxin, that have either zero or one arginine residue in their sequences. For protein ions having no arginine, we observe multiple b/y complementary fragment ion pairs (CFIP) by MALDI-MS/MS post-source decay demonstrating that the ionizing proton is located at multiple locations amongst the packet of protein precursor ions being analyzed. By contrast, for protein ions having one arginine, we observe little or no CFIP, and almost every fragment ion has the arginine residue in its sequence. This preferential proton sequestration is presumably due to the higher gas phase basicity of arginine compared to lysine, although lysine residues are often more numerous than arginine residues. As this phenomenon has been noted previously in the ionization of tryptic peptides by MALDI where the basic residue (K or R) is located exclusively at the C-terminus (if there are no missed proteolytic cleavages), we conclude that rapid proton transfer in the gas phase occurs via protein/matrix collisions in the MALDI plume. Upon proton transfer to the side-chain of an arginine residue, the proton is effectively immobilized by its guanidino functional group. An alternative explanation is proton exchange from the ionized side-chain of a lysine to the side-chain of the arginine in the metastable ion.

Proteomic Analysisof Food Allergens by MALDI TOF/TOF Mass Spectrometry.

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is largely recognized as an important tool in the analysis of many biomolecules such as proteins and peptides. The MS analysis of digested peptides to identify a protein or some of its modifications is a key step in proteomics. MALDI-MS is well suited for the peptide mass fingerprinting (PMF) technique, as well as selected fragmentation of various precursors using collisional-induced dissociation (CID) or post-source decay (PSD).In the last few years, MALDI-MS has played a significant role in food chemistry, especially in the detection of food adulterations, characterization of food allergens, and investigation of protein structural modifications induced by various industrial processes that could be an issue in terms of food quality and safety.Here, we present simple extraction protocols of allergenic proteins in food commodities such as milk, egg, hazelnut , and lupin seeds. Classic bottom-up approaches based on Sodium Dodecyl Sulphate(SDS) gel electrophoresis separation followed by in-gel digestion or direct in-solution digestion of whole samples are described. MALDI-MS and MS /MS analyses are discussed along with a comparison of data obtained by using the most widespread matrices for proteomic studies, namely, α-cyano-4-hydroxy-cinnamic acid (CHCA) and α-cyano-4-chloro-cinnamic acid (CClCA). The choice of the most suitable MALDI matrix is fundamental for high-throughput screening of putative food allergens.

Dissociation Pattern of Sodiated Amide Peptides as a Tool for De Novo Sequencing.

As part of the de novo sequencing issue, new approaches have to be found to sequence small natural peptides (<15-20 residues), which often present amino acid compositions, inducing merely singly charged species, that are quite difficult to thoroughly fragment under low-energy activation conditions in MS/MS experiments. Cationization by alkali metals, like Na+, followed by collision-induced dissociations (CID) or the postsource metastable decay (PSD) of such cationized molecular ions was found to improve the sequence coverage of native peptides through the formation of [bn-1 + Na + OH]+ ions issued from C-terminal residue exclusion. Concerned by the identification of peptides with a C-terminal amide, the fragmentation pattern of their sodiated molecular ions was investigated. In contrast to the peptides featuring unmodified C-termini, the C-terminal loss did not occur, with the amide function triggering different fragmentation pathways. However, several residues, such as aspartic acid (D), glutamic acid (E), and arginine (R), influenced the dissociation of fixed-charge sodiated ions similarly to protonated peptides; more surprisingly, serine (S), threonine (T), and tyrosine (Y), which exhibit a hydroxyl function on their side chains, showed a very peculiar behavior that could help de novo peptide sequencing.

Polypeptide backbone cleavage on the C-terminal side of asparagine residues of metastable protein ions analyzed by MALDI-TOF-TOF-MS/MS and post-source decay

The gas phase dissociation of B-subunits of Shiga toxin 2 (Stx2) subtypes expressed by pathogenic Escherichia coli have been analyzed using antibiotic induction, MALDI-TOF-TOF tandem mass spectrometry and post-source decay (PSD). Two Stx2 subtypes (a and c) are distinguished by two amino acid substitutions involving aspartic acid (D), asparagine (N) and alanine (A) residues. In addition to polypeptide backbone cleavage (PBC) on the C-terminal side of D and glutamic acid (E) residues by the aspartic acid effect (AAE) fragmentation mechanism, PBC is also observed on the C-terminal side of N-residues. It is estimated that N-residues are at least an order-of-magnitude less efficient than D-residues at PBC. As the side-chains of D and N residues are of equal length, the difference in PBC efficiency is likely due to differences in the gas phase acidities (ΔΔHacid ≈ 0.4 eV) of their respective side-chain functional groups: [−(CO)OH] for D versus [−(CO)NH2] for N. It is proposed that the AAE mechanism for N-residues results in the formation of a b-type fragment with a 2,5-pyrrolidinedione (or succinimide) end-group at its C-terminus similar to previous proposals that predict formation of a b-type fragment with a 2,5-furanedione (or succinic anhydride) end-group for D-residues. As a D ↔ N substitution differs in mass by only 1 Da, the b-fragment would also differ by 1 Da (if there are no other residue substitutions) and the complementary y-type fragment would have exactly the same mass. In consequence, the relative abundance of fragment ions caused by a D versus N residue might be a better indicator as to which residue was responsible for PBC rather than relying solely upon fragment ion m/z for this determination.

Identification of Proteins Using Four Methods of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

An upper-division undergraduate- or graduate-level laboratory experiment, challenging students to identify bovine serum albumin, equine myoglobin, bovine calmodulin, and bovine cytochrome c, uses four methods of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS): linear positive, in-source decay, peptide mass fingerprint, and postsource decay. Individual hands-on experience with each method is provided in a three week experiment. The importance of sequencing proteins/peptides when identifying proteomic targets using MALDI-TOF MS is emphasized.

Aniline derivative/DHB/alkali metal matrices for reflectron mode MALDI-TOF and TOF/TOF MS analysis of unmodified sialylated oligosaccharides and glycopeptides

Sialylglycoconjugates play biologically important roles in nature. The labile nature of the sialic acid residue in matrix-assisted laser desorption/ionization–mass spectrometry (MALDI-MS) analysis demands additional modification processes of the carboxylate group to avoid in-source or post-source decay. This paper reports a versatile and high-sensitivity matrix system, aniline derivative/2,5-dihydroxybenzoic acid/alkali metal salt, for MALDI-MS analysis of sialyloligosaccharides and sialylglycoconjugates without any modifications. A simple adduct ion signal was obtained from the femtomole range of the analytes tested with the new matrix system by MALDI-MS in reflectron mode. Besides, the laser power-dependent in-source decay and post-source decay pattern of the sialylated analytes with this matrix system allows a pseudo MS3 strategy for in-depth sequencing studies of the analytes.

Characterisation of triacylglycerols from bovine milk fat fractions with MALDI-TOF-MS fragmentation

In this study, we used MALDI-TOF-MS to profile and characterise the triacylglycerol (TAG) species of anhydrous bovine milk fat (AMF) and its low melting (olein) and high melting (stearin) fractions obtained by dry fractionation. Silver-ion solid phase extraction (Ag+-SPE) cartridges were utilised to separate the TAGs according to saturation degree. Then, several TAG species were selected and fragmented via post-source decay (PSD) fragmentation. MALDI-TOF-MS TAG profiles and fragmentation patterns were compared to the TAG and fatty acid (FA) compositions obtained by gas chromatography-flame ionization detector (GC-FID). We found that, olein was rich in medium length chain TAG species like CN38:0 and CN40:1, whereas stearin was rich in saturated long chain TAG species from CN42:0 to CN52:0. Separation of the TAGs based on saturation degree allowed successful selection of the TAG parent-ion for fragmentation by eliminating the interferences of TAG species that have the same carbon number but vary in number of double bonds. The TAG fragmentation patterns indicated significant differences between AMF, olein and stearin as a result of the dry fractionation process. Compared to AMF, olein yielded in higher fragments of short-chain saturated and middle-chain unsaturated FAs. Whereas, stearin yielded in saturated and monounsaturated long chain FA fragments. Fragmentation of unsaturated long chain TAGs showed that the TAGs in olein contained more C18:1 and C18:2 than that of AMF and stearin. Stearin on the other hand, contained higher amount of TAG species containing C16:0. These results were in line with the FA compositions obtained from GC-FID and suggest that Ag+-SPE cartridges coupled with MALDI-TOF-MS offer an informative and practical approach to characterise fats and oils with complex TAG composition.

Lipid Profile Changes During the Development of Artemia franciscana, From Cysts to the First Two Naupliar Stages.

The brine shrimp Artemia is an interesting experimental system for studies of developmental processes. Hatching of dormant cysts gives rise to shrimp larvae called nauplii, characterized by numerous naupliar stages representing the first forms of brine shrimp life cycle. Here combined Thin Layer Chromatography (TLC) and Matrix-Assisted Laser Desorption Ionization-Time-of-Flight/Mass Spectrometry (MALDI-TOF/MS) analyses have been performed to gain information on the lipid profiles of cysts and two naupliar stages. Lipid bands isolated after preparative TLC of the lipid extracts have been analyzed to detect various species of each lipid class; in addition Post-Source Decay (PSD) analyses allowed the identification of phospholipid chains. We compared the relative abundance of various polar and neutral lipid species in the lipid extracts, proving for the first time that during the development of nauplii there is an increase of cardiolipin (CL) and lysophospholipid levels; in parallel, the amount of phosphatidylcholine (PC) decreases. In addition, as regards neutral lipids, we found an increase of diacylglycerols (DAGs) in correspondence of the decrease of triacylglycerols (TAGs). Data reflect the fact that naupliar stages, being an active form of life, are more metabolically active and offer a platform to develop further studies on the importance of lipid metabolic pathways and bioactive lipids during the development.

Top-down and middle-down proteomic analysis of Shiga toxin using MALDI-TOF-TOF mass spectrometry

The method describes a step-by-step process for analysis of putative Shiga toxin-producing Escherichia coli (STEC) for expression of Shiga toxin (Stx). The technique utilizes antibiotic induction, mass spectrometry and top-down/middle-down proteomic analysis. Stx expression is induced by overnight culturing of a STEC strain on Luria-Bertani agar (LBA) supplemented with DNA-damaging antibiotics. Culturing on agar media avoids sample contamination from salts, small molecules, peptides, etc. present in broth media that would interfere with protein ionization by matrix-assisted laser desorption/ionization (MALDI). No mechanical lysis of bacterial cells is required to release the toxin as the antibiotic triggers the lytic cycle of the bacteriophage resulting in toxin expression and bacterial cell lysis. Unfractionated samples are analyzed by MALDI-time-of-flight-time-of-flight (MALDI-TOF-TOF) mass spectrometry and tandem mass spectrometry (MS/MS) using post-source decay (PSD). New features of the method are the following.•Each putative STEC strain is systematically screened for toxin expression using two different antibiotics at two different concentrations: ciprofloxacin at 10 and 20 ng mL−1 and mitomycin-C at 800 and 1200 ng mL−1 to determine the optimal antibiotic and concentration for toxin expression for each strain.•The grid-to-source voltage of MALDI-TOF-TOF is optimized to maximize PSD efficiency.

Software for top-down proteomic identification of a plasmid-borne factor (and other proteins) from genomically sequenced pathogenic bacteria using MALDI-TOF-TOF-MS/MS and post-source decay

A plasmid-borne factor (hypothetical protein) was identified in three Shiga toxin-producing Escherichia coli O113:H21 strains using antibiotic-induction, MALDI-TOF-TOF tandem mass spectrometry (MS/MS), post-source decay (PSD) and top-down proteomic analysis. The plasmid-encoded factor was identified from three pairs of complementary fragment ions (b/y) which were also used to obtain a more accurate calculation of the mass of the protein than that possible from MS analysis. A software application tool was developed to rapidly search amino acid sequences from whole genome sequencing-derived data to match the observed protein mass and fragment ions on the assumption that the fragment ions are the result of polypeptide backbone cleavage on the C-terminal side of aspartic acid and glutamic acid residues, i.e. aspartic acid effect. Manual inspection and top-down proteomic analysis confirmed the correctness of the identification of this protein using this new application tool. Although the function of the plasmid-borne factor is not known, its antibiotic-induced expression may suggest a role in antimicrobial stress. This approach was also used to identify three highly conserved bacterial cold-shock proteins: CspC, CspE, CsbD from one of the STEC strains. In addition to polypeptide backbone cleavage, metastable CsbD showed multiple small dissociative losses perhaps suggesting ammonia loss from the four arginine residues in its sequence. This phenomenon had been previously observed for metastable ubiquitin which also has four arginine residues.

Rapid analysis of ricin using hot acid digestion and MALDI-TOF mass spectrometry.

Ricin is a protein toxin of considerable interest in forensics. A novel strategy is reported here for rapid detection of ricin based on microwave-assisted hot acid digestion and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Ricin samples are subjected to aspartate-selective hydrolysis, and biomarker peptide products are characterized by mass spectrometry. Spectra are obtained using post source decay and searched against a protein database. Several advantages are offered by chemical hydrolysis, relative to enzymatic hydrolysis, notably speed, robustness, and the production of heavier biomarkers. Agglutinin contamination is reliably recognized, as is the disulfide bond strongly characteristic of ricin.