Optimization of a MALDI TOF-TOF mass spectrometer for intact protein analysis

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.

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

RATIONALE

Pathogenic 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.

METHODS

Protein 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.

RESULTS

Shiga 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.

CONCLUSIONS

TDP 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.

Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section

The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.

Booster-microchannel plate (BMCP) detector for signal amplification in MALDI-TOF mass spectrometry for ions beyond m/z 50 000

Top-down proteomics deals with the characterization of intact biomolecules, which reduces the sample complexity and facilitates the detection of modifications at the protein level. The combination of the matrix-assisted laser desorption/ionization (MALDI) technique with time-of-flight (TOF) mass analysis allows for the generation of gaseous ions in low charge states from high-mass biomolecules, followed by their mass-to-charge ratio (m/z) separation, as high-mass ions drift down the flight tube more slowly than lighter ones. However, the detection efficiency of conventional microchannel plate (MCP) detectors is strongly reduced with decreasing ion velocity-corresponding to an increase in ion mass-which impedes the reliable detection of high-mass biomolecules. Herein, we present a simple modification of the MCP detector that allows for the amplification of the signal from ionized proteins of up to m/z 150 000. Two circular electrodes were assembled in front of the conventional detector and set to negative electrical voltages to affect the positively charged ions directly before they impinge on the MCP, possibly through a combination of a velocity boost and ion optical effects. In the present study, three booster electrode configurations were experimentally tested to maximize the signal intensification. Compared to the conventional MCP assembly, the signal intensity was amplified in a proof-of-concept experiment by a factor of 24.3 and of 10.7 for the singly charged BSA ion (m/z 66 400) and for the singly charged IgG ion (m/z 150 000), respectively, by applying the booster-MCP (BMCP) detector.

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.

Diversity, structure and regulation of microbial metallothionein: metal resistance and possible applications in sequestration of toxic metals

Metallothioneins (MTs) are a group of cysteine-rich, universal, low molecular weight proteins distributed widely in almost all major taxonomic groups ranging from tiny microbes to highly organized vertebrates. The primary function of this protein is storage, transportation and binding of metals, which enable microorganisms to detoxify heavy metals. In the microbial world, these peptides were first identified in a cyanobacterium Synechococcus as the SmtA protein which exhibits high affinity towards rising level of zinc and cadmium to preserve metal homeostasis in a cell. In yeast, MTs aid in reserving copper and confer protection against copper toxicity by chelating excess copper ions in a cell. Two MTs, CUP1 and Crs5, originating from Saccharomyces cerevisiae predominantly bind to copper though are capable of binding with zinc and cadmium ions. MT superfamily 7 is found in ciliated protozoa which show high affinity towards copper and cadmium. Several tools and techniques, such as western blot, capillary electrophoresis, inductively coupled plasma, atomic emission spectroscopy and high performance liquid chromatography, have been extensively utilized for the detection and quantification of microbial MTs which are utilized for the efficient remediation and sequestration of heavy metals from a contaminated environment.

Mass Spectrometric (MS) Analysis of Proteins and Peptides

The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.

Microalgal Metallothioneins and Phytochelatins and Their Potential Use in Bioremediation

The persistence of heavy metals (HMs) in the environment causes adverse effects to all living organisms; HMs accumulate along the food chain affecting different levels of biological organizations, from cells to tissues. HMs enter cells through transporter proteins and can bind to enzymes and nucleic acids interfering with their functioning. Strategies used by microalgae to minimize HM toxicity include the biosynthesis of metal-binding peptides that chelate metal cations inhibiting their activity. Metal-binding peptides include genetically encoded metallothioneins (MTs) and enzymatically produced phytochelatins (PCs). A number of techniques, including genetic engineering, focus on increasing the biosynthesis of MTs and PCs in microalgae. The present review reports the current knowledge on microalgal MTs and PCs and describes the state of art of their use for HM bioremediation and other putative biotechnological applications, also emphasizing on techniques aimed at increasing the cellular concentrations of MTs and PCs. In spite of the broad metabolic and chemical diversity of microalgae that are currently receiving increasing attention by biotechnological research, knowledge on MTs and PCs from these organisms is still limited to date.

Intact cell MALDI-TOF mass spectrometry, a promising proteomic profiling method in farm animal clinical and reproduction research

The objective of this review is to provide new insights into the possible use of a proteomic method known as Intact Cell Matrix-Assisted Laser Desorption-ionization Time-Of-Flight Mass Spectrometry (ICM-MS) in animal clinical research. Here, we give an overview of the basics of this technique, its advantages and disadvantages compared with other proteomic approaches, past applications and future perspectives. A special emphasis on its implementation in animal reproduction science is given, including examples of the reliable use of ICM-MS on fertility screening. In mammals, the ICM-MS profiles from pig epididymal spermatozoa reflect the proteome changes that they undergo during epididymal maturation and could be associated with the acquisition of fertilizing ability. In chicken, using adequate pre-processing and bioinformatics analysis tools, sperm ICM-MS profiles showed characteristic spectral features that allowed their classification according to their actual fertilizing ability. The association of ICM-MS and Top-down proteomic strategies allowed the identification of chicken fertility biomarkers candidates such as protein vitelline membrane outer layer protein 1 (VMO-1) and avian beta-defensin 10 (AvBD10). In female reproduction, a similar approach on ovarian follicular cells allowed the identification of specific markers of oocyte maturation in the oocyte and surrounding cumulus cells. Altogether, these results indicate that ICM-MS profiling could be a suitable approach for molecular phenotyping of male and female gametes.

Elucidating Branching Topology and Branch Lengths in Star-Branched Polymers by Tandem Mass Spectrometry

Tandem mass spectrometry (MS²) has been employed to elucidate the topology and branching architecture of star-branched polyethers. The polymers were ionized by matrix-assisted laser desorption/ionization (MALDI) to positive ions and dissociated after leaving the ion source via laser-induced fragmentation. The bond scissions caused under MALDI-MS² conditions occur preferentially near the core-branch joining points due to energetically favorable homolytic and heterolytic bond cleavages near the core and release of steric strain and/or reduction of crowding. This unique fragmentation mode detaches complete arms from the core generating fragment ion series at the expected molecular weight of each branch. The number of fragment ion distributions observed combined with their mass-to-charge ratios permit conclusive determination of the degree of branching and the corresponding branch lengths, as demonstrated for differently branched homo- and mikto-arm polyether stars synthesized via azide-alkyne click chemistry. The results of this study underscore the utility of MS² for the characterization of branching architecture and branch lengths of (co) polymers with two or more linear chains attached to a functionalized central core.

Whole cell matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of Leptospira spp. in Thailand and Lao PDR

Leptospirosis is a zoonosis with a worldwide distribution, caused by pathogenic spirochetes of the genus Leptospira. The classification and identification of leptospires can be conducted by both genotyping and serotyping which are time-consuming and established in few reference laboratories. This study used matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as rapid and accurate tool for the identification of leptospires. The whole cell protein spectra of 116 Leptospira isolates including 15 references Leptospira spp. (pathogenic, n = 8; intermediate, n = 2; non-pathogenic, n = 5) and 101 Leptospira spp. clinical isolates was created as an in-house MALDI-TOF MS database. Ninety-seven clinical isolates from Thailand and Laos was validated with these protein spectra and revealed 98.9% correct identification when compared with 16S rRNA gene sequences method. Moreover, MALDI-TOF MS could identify spiked leptospires whole cell in urine. Biomarkers for differentiation of leptospires phylogeny and specific protein spectra for most found Leptospira spp. in this area (L. interrogans, L. kirschneri, L. borgpetersenii) based on MALDI-MS algorithm were demonstrated.

Intact cell MALDI-TOF mass spectrometric analysis of Chroococcidiopsis cyanobacteria for classification purposes and identification of possible marker proteins

Cyanobacteria represent a bacterial phyllum characteristic by the ability to photosynthesize. They are potentially applicable for the production of useful compounds but may also cause poisoning or at least health problems as they can produce cyanotoxins. The introduction of a fast methodology is important not only for fundamental taxonomic purposes, but also for reliable identifications in biological studies. In this work, we have used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells to study Chroococcidiopsis strains. A library of the obtained reference mass spectra containing characteristic peptide/protein profiles was examined by software tools to characterize similarities and differences applicable for diagnostics and taxonomy. Both a similarity tree and heat map constructed from the mass spectrometric data proved consistent with 16S rRNA sequencing results. We show as novelty that a binary matrix combining ferulic and sinapinic acids performs well in acquiring reproducible mass spectra of cyanobacteria. Using the matrix solvent, a protein extraction from cells was done. After polyacrylamide gel electrophoresis, the separated protein fractions were in-gel digested and the resulting peptides analyzed by liquid chromatography coupled with tandem mass spectrometry. For the first time, photosystem protein components, phycobilisome proteins, electron transport proteins, nitrogen-metabolism and nucleic acids binding-proteins, cytochromes plus other enzymes and various uncharacterized proteins could be assigned to characteristic peaks in the mass spectrometric profiles and some of them suggested as markers in addition to 30S and 50S ribosomal proteins known from previous studies employing intact cell mass spectrometry of microorganisms.

Applications of MALDI-TOF mass spectrometry in clinical proteomics

INTRODUCTION

The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics. Areas covered: This review aims to provide an updated overview of MALDI-TOF MS applications in clinical proteomics. The most relevant features of this analysis have been discussed, highlighting both pre-analytical and analytical factors that are crucial in proteomics studies. Particular emphasis is placed on biofluids proteomics for biomarkers discovery and on recent progresses in clinical microbiology, drug monitoring, and minimal residual disease (MRD). Expert commentary: Despite some analytical limitations, the latest technological advances together with the easiness of use, the low time and low cost consuming and the high throughput are making MALDI-TOF MS instruments very attractive for the clinical practice. These features offer a significant potential for the routine of the clinical laboratory and ultimately for personalized medicine.

Anatomical-Molecular Distribution of EphrinA1 in Infarcted Mouse Heart Using MALDI Mass Spectrometry Imaging

EphrinA1 is a tyrosine kinase receptor localized in the cellular membrane of healthy cardiomyocytes, the expression of which is lost upon myocardial infarction (MI). Intra-cardiac injection of the recombinant form of ephrinA1 (ephrinA1-Fc) at the time of ligation in mice has shown beneficial effects by reducing infarct size and myocardial necrosis post-MI. To date, immunohistochemistry and Western blotting comprise the only experimental approaches utilized to localize and quantify relative changes of ephrinA1 in sections and homogenates of whole left ventricle, respectively. Herein, we used matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) coupled with a time-of-flight mass spectrometer (MALDI/TOF MS) to identify intact as well as tryptic fragments of ephrinA1 in healthy controls and acutely infarcted murine hearts. The purpose of the present study was 3-fold: (1) to spatially resolve the molecular distribution of endogenous ephrinA1, (2) to determine the anatomical expression profile of endogenous ephrinA1 after acute MI, and (3) to identify molecular targets of ephrinA1-Fc action post-MI. The tryptic fragments detected were identified as the ephrinA1-isoform with 38% and 34% sequence coverage and Mascot scores of 25 for the control and MI hearts, respectively. By using MALDI-MSI, we have been able to simultaneously measure the distribution and spatial localization of ephrinA1, as well as additional cardiac proteins, thus offering valuable information for the elucidation of molecular partners, mediators, and targets of ephrinA1 action in cardiac muscle. Graphical Abstract ᅟ.

Human disease glycomics: technology advances enabling protein glycosylation analysis - part 1

INTRODUCTION

Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics). The technologies currently available for glycomics are becoming streamlined and standardized and many features of protein glycosylation can now be determined using instruments available in most protein analytical laboratories. Areas covered: This review focuses on the current glycomics technologies being commonly used for the analysis of the microheterogeneity of monosaccharide composition, sequence, branching and linkage of released N- and O-linked glycans that enable the determination of precise glycan structural determinants presented on secreted proteins and on the surface of all cells. Expert commentary: Several emerging advances in these technologies enabling glycomics analysis are discussed. The technological and bioinformatics requirements to be able to accurately assign these precise glycan features at biological levels in a disease context are assessed.

MALDI-LID-ToF/ToF analysis of statistical and diblock polyacrylate copolymers

We report the use of MALDI-LID-ToF/ToF utilising the laser induced dissociation (LID) fragmentation technique, which has been almost exclusively applied to protein/peptide analysis to date.

Identification of four cornua by ultra-performance liquid chromatography with time-of-flight mass spectrometry coupled with principal component analysis

An ultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry method coupled with principal component analysis was developed and applied to the identification of Cornu Antelopis, Cornu Bubali, Cornu Naemorhedi, and Cornu Bovis. The data obtained from the trypsin-digested samples were subjected to principal component analysis to classify these four cornua. Additionally, marker peptides of the cornua were determined by orthogonal partial least-squares discriminant analysis, and fragmentation tandem mass spectra of these marker peptides were evaluated. The results from this study indicate that the proposed method is reliable, and it has been successfully applied to the identification of variants of cornua commonly used in traditional Chinese medicine.

Design and development of caffeic acid conjugated with Bombyx mori derived peptide biomaterials for anti-aging skin care applications

This study examined the significant features of caffeic acid conjugated with peptide (APPPKK) to determine if it meets the requirements for a cosmetic anti-aging biomolecule.

Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometric analysis of lysozyme contained in hen egg white

As a natural antibacterial peptide, lysozyme (LZ) is widely used in medicine and the food industry. Despite many years of research on this compound, its new antibacterial properties are still to be determined. The primary aim of this work is to demonstrate the application of the matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectrometric analysis of LZ directly in hen egg white samples without extraction thereof. The egg white samples were kept over 10 weeks at room temperature and measured every week. The resulting positive and negative ion mass spectra were then compared to determine the intensity of the LZ mass peak. Storage of the egg white for over 10 weeks did not influence the LZ mass peak intensity (both positive and negative). It can be concluded that the LZ concentration in the egg white samples did not vary with time. The effect of the matrix/sample ratio on LZ detection was also examined, and it was found to be different in the case of positive and negative ionization. The mass peaks of LZ oligomeric forms were observed in all mass spectra, so the MALDI method could be used in subsequent studies.

Quantification of the PR-39 cathelicidin compound in porcine blood by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

RATIONALE

The PR-39 porcine cathelicidin occurs naturally in animal neutrophils. Its main function is antimicrobial activity, which potentially can be used in antibiotic treatments in veterinary medicine. Investigations concerning such a use require the detection and quantification of PR-39 in a given sample. The aim of this work is to determine the concentration of PR-39 contained in porcine blood.

METHODS

Prior to matrix-assisted laser desorption/ionization (MALDI) analysis, the porcine blood sample was subjected to crude extraction in order to release the active form of PR-39 from the neutrophil granules. Next, gel filtration chromatography was performed to separate PR-39 from other cathelicidins present in porcine blood. Positive ion MALDI time-of-flight (TOF) mass spectra of the resulting portion of lyophilisate with unknown PR-39 content were acquired in linear mode. To quantify PR-39 in the lyophilisate sample, the standard addition method was applied. The PR-39 concentration obtained in the lyophilisate sample was then converted into the peptide concentration in porcine blood.

RESULTS

The linear fit function of the constructed calibration curve indicates an excellent correlation between the PR-39 peak intensity and the added quantity of synthetic PR-39 (R(2) = 0.994) and a low relative standard deviation of the slope = 1.98%. From the x-intercept of the straight line, we estimated the PR-39 concentration in porcine blood to be 20.5 ± 4.6 ng/mL.

CONCLUSIONS

The MALDI method was successfully applied for the quantitative analysis of PR-39 found in porcine blood. Compared with other available methods, it is relatively easy, inexpensive and not time-consuming. Despite the method having lower accuracy than the enzyme-linked immunosorbent assay (ELISA), the results obtained here, by a much simpler method, are in good agreement with the literature data.

Measuring masses of large biomolecules and bioparticles using mass spectrometric techniques

Mass spectrometric techniques can measure the masses and fragments of large biomolecules and bioparticles.

Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometric analysis of intact proteins larger than 100 kDa

Effectively determining masses of proteins is critical to many biological studies (e.g. for structural biology investigations). Accurate mass determination allows one to evaluate the correctness of protein primary sequences, the presence of mutations and/or post-translational modifications, the possible protein degradation, the sample homogeneity, and the degree of isotope incorporation in case of labelling (e.g.¹³C labelling).

Electrospray ionisation (ESI) mass spectrometry (MS) is widely used for mass determination of denatured proteins, but its efficiency is affected by the composition of the sample buffer. In particular, the presence of salts, detergents, and contaminants severely undermines the effectiveness of protein analysis by ESI-MS. Matrix-assisted laser desorption/ionization (MALDI) MS is an attractive alternative, due to its salt tolerance and the simplicity of data acquisition and interpretation. Moreover, the mass determination of large heterogeneous proteins (bigger than 100 kDa) is easier by MALDI-MS due to the absence of overlapping high charge state distributions which are present in ESI spectra.

Here we present an accessible approach for analysing proteins larger than 100 kDa by MALDI-time of flight (TOF). We illustrate the advantages of using a mixture of two matrices (i.e. 2,5-dihydroxybenzoic acid and α-cyano-4-hydroxycinnamic acid) and the utility of the thin layer method as approach for sample deposition. We also discuss the critical role of the matrix and solvent purity, of the standards used for calibration, of the laser energy, and of the acquisition time. Overall, we provide information necessary to a novice for analysing intact proteins larger than 100 kDa by MALDI-MS.

Production of reliable MALDI spectra with quality threshold clustering of replicates

We present the first application of the quality threshold (QT) clustering algorithm to mass spectrometry (MS) data. The unique abilities of QT clustering to yield precision nodes that are commensurate with the mass measurement precision of the instrument are exploited to generate a consensus spectrum out of multiple replicate spectra. The spectral dot product and confidence intervals are used as a tool for evaluating the similarity and reproducibility between the consensus and replicates. The method is equally applicable to high and low resolution measurements. This paper demonstrates applications to linear spectra from a matrix assisted laser desorption ionization (MALDI) time of flight (TOF) instrument as well as peptide fragmentation data obtained from a TOF/TOF after unimolecular decomposition. The advantages of clustering to mitigate the inherent precision the shortcomings of MALDI data are discussed.

Protein signatures for survival and recurrence in metastatic melanoma

Patients with melanoma metastatic to regional lymph nodes exhibit a range in tumor progression, survival, and treatment. Current approaches to stratify patients with this stage of disease predominantly involve clinical and histological methods. Molecular classification thus far has focused almost exclusively on genetic mutations. In this study, proteomic data from 69 melanoma lymph node metastases and 17 disease free lymph nodes acquired by histology-directed MALDI imaging mass spectrometry were used to classify tumor from control lymph node and to molecularly sub-classify patients with stage III disease. From these data, 12 survival associated protein signals and 3 recurrence associated signals in the acquired mass spectra were combined to generate a multiplex molecular signature to group patients into either poor or favorable groups for recurrence and survival. Proteins represented in the signature include cytochrome c, s100 A6, histone H4, and cleaved forms of thymosin β-4, thymosin β-10, and ubiquitin. In total over 40 protein signals from the tissue were identified.

Top-down protein identification/characterization of a priori unknown proteins via ion trap collision-induced dissociation and ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer

The identification and characterization of a priori unknown proteins from an Escherichia coli (E. coli) soluble protein lysate using ion trap collision-induced dissociation of intact protein ions followed by ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer is illustrated. The procedure involved the submission of uninterpreted product ion spectra to a peak-picking program and then to ProSightPTM for searching against an E. coli database. Examples are provided for the identification and characterization of both modified and unmodified unknown proteins with masses up to approximately 28 kDa. The availability of protein intact mass along with sequence information makes possible the characterization of proteins with post-translational modifications, such as disulfide linkages, as well as protein isoforms whose sequences are absent from a database, provided that a related form of the gene product is present in the database. This work demonstrates that the quadrupole/time-of-flight platform, in conjunction with ion-ion proton transfer reactions, can be adapted to obtain primary structure information from entire protein ions, rather than simply N- or C-terminal information from low mass-to-charge products, for proteins as large as several tens of kilodaltons.

Toward top-down determination of PEGylation site using MALDI in-source decay MS analysis

A novel matrix assisted laser desorption/ionization (MALDI)-based mass spectrometric approach has been evaluated to rapidly analyze a custom designed PEGylated peptide that is 31 residues long and conjugated with 20 kDa linear polyethylene glycol (PEG) at the side chain of Lys. MALDI-TOF MS provided sufficiently high resolution to allow observation of each of the oligomers of the heterogeneous PEGylated peptide (m/Deltam of ca. 500), while a typical ESI-MS spectrum of this molecule was extremely complex and unresolved. Reflector in-source decay (reISD) analysis using MALDI-TOF MS was attempted to identify the PEGylation site at intact molecular level without any sample treatment. An reISD spectrum of the free peptide was observed with abundant c-, y-, and [z + 2]-fragment ion series, whereas, in the fragmented PEGylated peptide, the fragment ion series were truncated at the residue where PEG was attached. Therefore, a direct comparison of these top-down reISD spectra suggested the location of the PEGylation site. Results from this study demonstrate a clear analytical utility of the ISD technique to characterize structural aspects of heterogeneous biomolecules.

Top-down proteomics on a high-field Fourier transform ion cyclotron resonance mass spectrometer

Mass spectrometry is the tool of choice for sequencing peptides and determining the sites of posttranslational modifications; however, this bottom-up approach lacks in providing global information about the modification states of proteins including the number and types of isoforms and their stoichiometry. Recently, various techniques and mass spectrometers, such as high-field Fourier Transform Ion Cyclotron Resonance (FTICR) mass spectrometers, have been developed to study intact proteins (top-down proteomics). While the protein molecular mass and the qualitative and quantitative information about protein isoforms can be revealed by FTICR-MS analysis, their primary structure (including the identification of modifications and their exact locations in the amino acid sequence) can directly be determined using the MS/MS capability offered by the FTICR mass spectrometer. The distinct advantage of top-down methods are that modifications can be determined for a specific protein isoform rather than for peptides belonging to one or several isoforms. In this chapter, we describe different top-down proteomic approaches enabled by high-field (7, 9.4, and 12 T) FTICR mass spectrometers, and their applicability to answer biological and biomedical questions. We also describe the use of the free flow electrophoresis (FFE) to separate proteins prior to top-down mass spectrometric characterization.

Fragmentation of multiply-charged intact protein ions using MALDI TOF-TOF mass spectrometry

Top down proteomics in a TOF-TOF instrument was further explored by examining the fragmentation of multiply charged precursors ions generated by matrix-assisted laser desorption ionization. Evaluation of sample preparation conditions allowed selection of solvent/matrix conditions and sample deposition methods to produce sufficiently abundant doubly and triply charged precursor ions for subsequent CID experiments. As previously reported, preferential cleavage was observed at sites C-terminal to acidic residues and N-terminal to proline residues for all ions examined. An increase in nonpreferential fragmentation as well as additional low mass product ions was observed in the spectra from multiply charged precursor ions providing increased sequence coverage. This enhanced fragmentation from multiply charged precursor ions became increasingly important with increasing protein molecular weight and facilitates protein identification using database searching algorithms. The useable mass range for MALDI TOF-TOF analysis of intact proteins has been expanded to 18.2 kDa using this approach.

Matrix-assisted laser desorption/ionization mechanism study with dihydroxybenzoic acid isomers as matrices

Desorption and ionization efficiencies of matrix-assisted laser desorption/ionization (MALDI) for various biomolecules with different dihydroxybenzoic acid isomers were studied. No clear relationships were observed between MALDI biomolecule signals vs. gas-phase basicity, proton affinity and ionization potential. This indicates the the gas-phase protonation mechanism is not adequate to explain the observed results.

Effect of the addition of diammonium citrate to alpha-cyano-4-hydroxycinnamic acid (CHCA) matrix for the detection of phosphorylated peptide in phosphorylation reactions using cell and tissue lysates

The ionization of phosphorylated peptides is usually suppressed by non-phosphorylated peptides when alpha-cyano-4-hydroxycinnamic acid (CHCA) is used as a matrix for matrix-assisted laser desorption/ionization-time-of-Flight (MALDI-TOF) mass spectrometry analysis. In the present study, we examined the effect of diammonium citrate addition to the CHCA matrix on the detection of phosphorylated peptides. Substrates for protein kinase C (PKC) and c-Src were synthesized and phosphorylated by reaction with cell and tissue lysate samples. The addition of diammonium citrate to the CHCA matrix increased the sensitivity for distinguishing phosphorylated peptides from background noise. However, the effect depended on substrate concentration.

Fragmentation of leucine enkephalin as a function of laser fluence in a MALDI TOF-TOF

The effects of laser fluence on ion formation in MALDI were studied using a tandem TOF mass spectrometer with a Nd-YAG laser and alpha-cyano hydrocinnamic acid matrix. Leucine enkephalin ionization and fragmentation were followed as a function of laser fluence ranging from the threshold of ion formation to the maximum available, that is, about 280-930 mJ/mm2. The most notable finding was the appearance of immonium ions at fluence values close to threshold, increasing rapidly and then tapering in intensity with the appearance of typical backbone fragment ions. The data suggest the presence of two distinct environments for ion formation. One is associated with molecular desorption at low values of laser fluence that leads to extensive immonium ion formation. The second becomes dominant at higher fluences, is associated initially with backbone type fragments, but, at the highest values of fluence, progresses to immonium fragments. This second environment is suggestive of ion desorption from large pieces of material ablated from the surface. Arrhenius rate law considerations were used to estimate temperatures associated with the onset of these two processes.

Mass-tag technology responding to intracellular signals as a novel assay system for the diagnosis of tumor

A novel mass spectrometry-based assay system for determining protein kinase activity employing mass-tagged substrate peptide probes was used for the diagnosis of tumors. Two peptide probes (H-type and D-type) were synthesized containing the same substrate peptide sequence for protein kinase C (PKC). The molecular weights of the two probes differ because of the incorporation of deuterium into the acetyl groups of the D-type probe. The lysates of the normal and tumor tissue were prepared and reacted with the H- and D-type peptide probes, respectively. The PKC activities of the normal and tumor tissues can be compared simply and directly by calculating the phosphorylated ratio to each peptide probe, obtained from the peak intensity of the mass spectrum after mixing of the two reaction solutions. The phosphorylation ratio for the reaction of the H-type peptide probe with the tumor tissue lysate (B16 melanoma) was more than three times higher than that of the D type peptide probe with the normal skin tissue lysate. These results show that the novel assay system for detecting protein kinase activity using mass-tag technology can be a simple and useful means to profile protein kinase activity for cell or tissue lysate samples, and can be applied to the diagnosis of tumors.

Photodissociation at 193 nm of some singly protonated peptides and proteins with m/z 2000-9000 using a tandem time-of-flight mass spectrometer equipped with a second source for delayed extraction/post-acceleration of product ions

A tandem time-of-flight mass spectrometer was built for photodissociation (PD) of singly protonated peptides and small proteins generated by matrix-assisted laser desorption/ionization. PD was performed in a second source after deceleration of precursor ions. The delayed extraction/post-acceleration scheme was used for the product ions. For the PD at 193 nm of small singly protonated peptides, the present instrument showed much better sensitivity and resolution for product ions than the previous one (Moon JH, Yoon SH, Kim MS, Bull. Korean Chem. Soc. 2005; 26: 763) even though the overall spectral patterns obtained with the two instruments were similar. The present instrument was inferior in precursor ion selection and background noise level. PD was achieved for precursor ions as large as the singly protonated ubiquitin (m/z 8560.63), indicating that the photoexcitation is capable of supplying a sufficient amount of internal energy to dissociate large singly protonated proteins. As the precursor ion m/z increased, however, product ion signals deteriorated rather rapidly. As in the PD of small peptide ions with m/z around 1000, the types of the product ions generated from singly protonated peptides with m/z in the range 2000-4000 were mostly determined by the positions of arginine residues. Namely, a(n) and d(n) ions dominated when an arginine residue(s) was near the N-terminus while v(n), w(n), x(n) and y(n) dominated when the same residue(s) was near the C-terminus. In addition, d(n), v(n) and w(n) ions were generated according to the correlation rules previously observed in the collisionally activated dissociation. Isoleucine and leucine isomers could be easily distinguished based on the w(n) and d(n) ions.

Neuroproteomics: relevance to anxiety disorders

Despite advances in the treatment of anxiety disorders, there is a need for medications with greater efficacy and fewer side effects. Advances in techniques to facilitate high throughput, mass analysis of proteins potentially allows for new drug targets, with a shift in focus from membrane receptor proteins and enzymes of neurotransmitter metabolism to molecules in intracellular signal transduction and other pathways. A computerized literature search was done to collect studies on recently developed proteomic techniques and their application in psychiatric research. Particular techniques, such as two-dimensional electrophoresis, two-dimensional differential gel electrophoresis, isotope-coded affinity tags, and isotope tags for relative and absolute quantification, are reviewed. In addition, a combination of these techniques with MALDI-TOF/TOF and ESI-Q-TOF mass spectrometry analysis is discussed in relation to possible novel signaling pathways relevant to anxiety disorders, and to the development of biomarkers for the evaluation of these conditions.

A deflection system to reduce the interference from post-source decay product ions in photodissociation tandem time-of-flight mass spectrometry

A deflection system consisting of four deflectors was designed and used to reduce the interference from post-source decay (PSD) product ions in photodissociation (PD) tandem time-of-flight (TOF) mass spectrometry. For simple protonated peptides generated by matrix-assisted laser desorption/ionization, the presence of PSD product ions at the laser irradiation spot was found to noticeably alter the minor peaks in the PD spectra even though the major ones were hardly affected. Other benefits from the use of the deflection system such as the improvement in the resolving power in PSD tandem mass spectra are discussed.

Peptide photodissociation at 157 nm in a linear ion trap mass spectrometer

The photodissociation by 157 nm light of singly- and doubly-charged peptide ions containing C- or N-terminal arginine residues was studied in a linear ion trap mass spectrometer. Singly-charged peptides yielded primarily x- and a-type ions, depending on the location of the arginine residue, along with some related side-chain fragments. These results are consistent with our previous work using a tandem time-of-flight (TOF) instrument with a vacuum matrix-assisted laser desorption/ionization (MALDI) source. Thus, the different internal energies of precursor ions in the two experiments seem to have little effect on their photofragmentation. For doubly-charged peptides, the dominant fragments observed in both photodissociation and collisionally induced dissociation (CID) experiments are b- and y-type ions. Preliminary experiments demonstrating fragmentation of multiply-charged ubiquitin ions by 157 nm photodissociation are also presented.