Decoding protein modifications using top-down mass spectrometry

Top-down mass spectrometry is an emerging technology which strives to preserve the post-translationally modified forms of proteins present in vivo by measuring them intact, rather than measuring peptides produced from them by proteolysis. The top-down technology is beginning to capture the interest of biologists and mass spectrometrists alike, with a main goal of deciphering interaction networks operative in cellular pathways. Here we outline recent approaches and applications of top-down mass spectrometry as well as an outlook for its future.     

Detection of a novel variant human hemoglobin by electrospray ionization mass spectrometry

A novel hemoglobin variant was detected by electrospray ionization mass spectrometry. Hb Zurich-Hottingen is characterized by an Asn --> Ser replacement in the alpha-chain at position 9 as confirmed by DNA analysis. This hemoglobin variant is silent in isoelectric focusing, reversed-phase chromatography, and cation-exchange chromatography. The mutant alpha-chain was detectable only with electrospray mass spectrometry by its mass shift of -27 Da. The carrier was found to be heterozygous for the new hemoglobin variant. These results illustrate the power of ESI mass spectrometry for hemoglobin analysis.     

Applications of mass spectrometry for quantitation of DNA adducts

DNA adducts are formed when electrophilic molecules or free radicals attack DNA. 32P-postlabeling has been the most commonly used assay for quantitation of DNA adducts due mainly to its excellent sensitivity that allows quantitation at concentrations as low as approximately 1 adduct per 10(9) normal bases. Such methods, however, do not have the specificity desired for accurate and reliable quantitation, and are prone to produce false positives and artifacts. In the last decade, mass spectrometry in combination with liquid and gas chromatography has presented itself as a good alternative to these techniques since it can satisfy the need for specificity and reliability through the use of stable isotope-labeled internal standards and highly specific detection modes such as selected reaction monitoring and high-resolution mass spectrometry. In this article, the contribution of mass spectrometry to the quantitation of DNA adducts is reviewed with special emphasis on unique applications of mass spectrometry in the area of DNA adduct quantitation and recent applications with improvements in sensitivity.     

Multiple statistical analysis techniques corroborate intratumor heterogeneity in imaging mass spectrometry datasets of myxofibrosarcoma

MALDI mass spectrometry can generate profiles that contain hundreds of biomolecular ions directly from tissue. Spatially-correlated analysis, MALDI imaging MS, can simultaneously reveal how each of these biomolecular ions varies in clinical tissue samples. The use of statistical data analysis tools to identify regions containing correlated mass spectrometry profiles is referred to as imaging MS-based molecular histology because of its ability to annotate tissues solely on the basis of the imaging MS data. Several reports have indicated that imaging MS-based molecular histology may be able to complement established histological and histochemical techniques by distinguishing between pathologies with overlapping/identical morphologies and revealing biomolecular intratumor heterogeneity. A data analysis pipeline that identifies regions of imaging MS datasets with correlated mass spectrometry profiles could lead to the development of novel methods for improved diagnosis (differentiating subgroups within distinct histological groups) and annotating the spatio-chemical makeup of tumors. Here it is demonstrated that highlighting the regions within imaging MS datasets whose mass spectrometry profiles were found to be correlated by five independent multivariate methods provides a consistently accurate summary of the spatio-chemical heterogeneity. The corroboration provided by using multiple multivariate methods, efficiently applied in an automated routine, provides assurance that the identified regions are indeed characterized by distinct mass spectrometry profiles, a crucial requirement for its development as a complementary histological tool. When simultaneously applied to imaging MS datasets from multiple patient samples of intermediate-grade myxofibrosarcoma, a heterogeneous soft tissue sarcoma, nodules with mass spectrometry profiles found to be distinct by five different multivariate methods were detected within morphologically identical regions of all patient tissue samples. To aid the further development of imaging MS based molecular histology as a complementary histological tool the Matlab code of the agreement analysis, instructions and a reduced dataset are included as supporting information.     

Chemical modification of nucleic acids. Methylation of calf thymus DNA investigated by mass spectrometry and liquid chromatography

Mass spectrometry provides an extremely sensitive method for the identification and quantification of modified nucleosides and hence for determining chemical modifications of nucleic acids. When mass spectrometry is used in conjunction with a new high-performance liquid chromatographic system capable of separating 15 methylated and naturally occurring nucleosides, this allows the quantification of products of in vitro DNA methylation. With synthetic (2H3)methyl-labeled methylnucleosides as internal references, the distribution of methylated products formed when calf thymus DNA was reacted with N-methyl-N-nitrosourea(MeNU) was determined. Five modified products, 1-methyldeoxyadenosine(m1dA), 3-methyldeoxycytidine(m3dC), 7-methyldeoxyguanosine(m7dG), 3-methylthymidine(m3T) and O4-methylthymidine(m4T) were detected and the relative distributions were measured. The ability of mass spectrometry/mass spectrometry (tandem mass spectrometry) to increase specificity and sensitivity in this determination is demonstrated and its application to in vivo studies is suggested.     

Surface view of the lateral organization of lipids and proteins in lung surfactant model systems—A ToF-SIMS approach

The lateral organization of domain structures is an extremely significant aspect of biomembrane research. Chemical imaging by mass spectrometry with its recent advancement in sensitivity and lateral resolution has become a highly promising tool in biological research. In this review, we focus briefly on the instrumentation, working principle and important concepts related to time-of-flight secondary ion mass spectrometry followed by an overview of lipid/protein fragmentation patterns and chemical mapping. The key issues addressed are the applications of time-of-flight secondary ion mass spectrometry in biological membrane research. Additionally, we briefly review our recent investigations based on time-of-flight secondary ion mass spectrometry to unravel the lateral distribution of lipids and surfactant proteins in lung surfactant model systems as an example that highlights the importance of fluidity and ionic conditions on lipid phase behavior and lipid-protein interactions.     

Fast atom bombardment mass spectrometry of the anthocyanins violanin and platyconin

Fast atom bombardment mass spectrometry (FABMS) of the acylated anthocyanin violanin confirmed its molecular mass (919) and gave a fragmentation pattern in agreement with its known structure. FABMS of the more complex flower pigment platyconin gave its accurate molecular mass as 1421.3740 and a fragmentation pattern suggesting that platyconin is delphinidin 3-rutinoside-5-glucoside with two mols of glucosylcaffeic acid attached to the glucose moiety of rutinose in a branched-chain arrangement.     

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

A crucial part of a successful systems biology experiment is an assay that provides reliable, quantitative measurements for each of the components in the system being studied. For proteomics to be a key part of such studies, it must deliver accurate quantification of all the components in the system for each tested perturbation without any gaps in the data. This will require a new approach to proteomics that is based on emerging targeted quantitative mass spectrometry techniques. The PeptideAtlas Project comprises a growing, publicly accessible database of peptides identified in many tandem mass spectrometry proteomics studies and software tools that allow the building of PeptideAtlas, as well as its use by the research community. Here, we describe the PeptideAtlas Project, its contents and components, and show how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics.     

High-performance liquid chromatography coupled with tandem mass spectrometry applied for metabolic study of ginsenoside Rb1 on rat

Liquid chromatography coupled with mass spectrometry and tandem mass spectrometry has been applied to investigate the in vivo metabolism of ginsenoside Rb(1) in rat. Both positive electrospray ionization mass spectrometry and negative electrospray ionization mass spectrometry were used to identify the Rb(1) and its metabolites in rat plasma, urine, and feces samples. Oxygenation and deglycosylation were found to be the major metabolic pathways of Rb(1) in rat. A total of nine metabolites were detected in urine and feces samples collected after intravenous and oral administration. Deglycosylated metabolism of Rb(1) generated other ginsenosides as the major metabolites, such as Rd, Rg(3) or F(2), Rh(2), or C-K. This result indicates that the ginsenoside Rb(1) has many pharmacological activities and could be used as a prodrug.     

Protocol for the purification of proteins from biological extracts for identification by mass spectrometry

When a protein signal is selected by mass spectrometry as being a potential biomarker, it is necessary to formally identify it. This process involves separation of the protein in question and its identification by either peptide fingerprinting or tandem mass spectrometry sequencing. In the following pages, a simple and rapid protocol is described. Basically, the protocol consists of an initial rational selection of a few sorbents followed by alignment of these as a series of columns to obtain the purified target protein. This preparation is then submitted to electrophoresis, the band is excised and the trypsin digest is analyzed by either mass spectrometry (mass fingerprinting approach) or by LC-MS/MS (sequencing). The development of the process takes only a few days. Experimental data for the isolation and identification of proteins are discussed and two examples are shown.     

Mass spectrometry meets the challenge of understanding the complexity of the lipoproteome: recent findings regarding proteins involved in dyslipidemia and cardiovascular disease

Despite the fact that link between dyslipidemia and atherosclerosis was made over 100 years ago, atherosclerosis remains a major cause of morbidity and mortality worldwide. Major efforts focus towards understanding lipid metabolism, particularly by studying its particle compartments in circulation: the lipoproteins. In recent years, mass spectrometry has played an integral role in the deep sequencing of the lipoproteome and in metabolism studies conducted in vivo. This review highlights the path of lipoprotein research towards state-of-the-art mass spectrometry with special emphasis on the method of selected reaction monitoring and its impact on apolipoprotein metabolism studies. Also presented is what is expected for the lipoprotein field with the recent advent of high resolution/accurate mass parallel reaction monitoring mass spectrometry. The benefits of high resolution/accurate mass measurements are demonstrated by example instrument workflows and by detailing a novel method to quantify very low levels of circulating proprotein convertase subtilisin-kexin type 9 in rabbit. It is anticipated that future clinical studies or clinical trials aimed to treat dyslipidemia by manipulating key regulatory proteins will benefit from the new and exciting opportunities afforded by the latest technologies in mass spectrometry.     

Practical aspects of liquid chromatography-mass spectrometry (LS-MS) of lipids

Techniques for coupling liquid chromatography with mass spectrometry are reviewed and an interface is described for the analysis of lipids by mass spectrometry. The interface for coupling liquid chromatography with mass spectrometry for lipid analysis is based on the moving wire transport principle using an endless stainless steel belt of novel construction. After evaporation of the solvent, the solute remains as a residue on the belt which transports it into a reactor where it is volatilized by evaporation or conversion to hydrocarbons. The volatile compounds are then fed into the source of a chemical ionization mass spectrometer for mass analysis by total or single ion monitoring as well as for structural identification or compositional analysis. The sensitivity of the system was approx. 1 mg per component separated in the eluate of a high efficiency column. The capabilities of the interface were demonstrated by its application to reference compounds representative of triglycerides, sterols, steryl esters, glyceryl ethers, glyceryl ether diesters, glycerophosphatides, sphingolipids, prostaglandins and fatty acid methyl esters. It also was applied to the analysis of methyl ester ozonides to demonstrate the use of LC-MS for the localization of double bonds in unsaturated fatty acids.     

Identification and quantification of 8,5'-cyclo-2'-deoxy-adenosine in DNA by liquid chromatography/ mass spectrometry

Recent studies suggested that 8,5'-cyclo-2'-deoxyadenosine may play a role in diseases with defective nucleotide-excision repair. This compound is one of the major lesions, which is formed in DNA by hydroxyl radical attack on the sugar moiety of 2'-deoxyadenosine. It is likely to be repaired by nucleotide-excision repair rather than by base-excision repair because of a covalent bond between the sugar and base moieties. We studied the measurement of 8,5'-cyclo-2'-deoxyadenosine in DNA by liquid chromatography/isotope-dilution mass spectrometry. A methodology was developed for the analysis of 8,5'-cyclo-2'-deoxyadenosine by liquid chromatography in DNA hydrolyzed to nucleosides by a combination of four enzymes, i.e., DNase I, phosphodiesterases I and II, and alkaline phosphatase. Detection by mass spectrometry was performed using atmospheric pressure ionization-electrospray process in the positive ionization mode. Results showed that liquid chromatography/isotope-dilution mass spectrometry is well suited for identification and quantification of 8,5'-cyclo-2'-deoxyadenosine in DNA. Both (5'R)- and (5'S)-diastereomers of 8,5'-cyclo-2'-deoxyadenosine were detected. The level of sensitivity of liquid chromatography/mass spectrometry with selected-ion monitoring amounted to 2 fmol of this compound on the column. The yield of 8,5'-cyclo-2'-deoxyadenosine was measured in DNA in aqueous solution exposed to ionizing radiation at doses from 2.5 to 80 Gray. Gas chromatography/mass spectrometry was also used to measure this compound in DNA. Both techniques yielded similar results. The yield of 8,5'-cyclo-2'-deoxyadenosine was comparable to the yields of some of the other major modified bases in DNA, which were measured using gas chromatography/mass spectrometry. The measurement of 8,5'-cyclo-2'-deoxyadenosine by liquid chromatography/mass spectrometry may contribute to the understanding of its biological properties and its role in diseases with defective nucleotide-excision repair.     

Mass spectrometry detection of monkeypox virus: Comprehensive coverage for ranking the most responsive peptide markers

The recent and sudden outbreak of monkeypox in numerous non-endemic countries requires expanding its surveillance immediately and understanding its origin and spread. As learned from the COVID-19 pandemic, appropriate detection techniques are crucial to achieving such a goal. Mass spectrometry has the advantages of a rapid response, low analytical interferences, better precision, and easier multiplexing to detect various pathogens and their variants. In this proteomic dataset, we report experimental data on the proteome of the monkeypox virus (MPXV) recorded by state-of-the-art shotgun proteomics, including data-dependent and data-independent acquisition for comprehensive coverage. We highlighted 152 viral proteins, corresponding to an overall proteome coverage of 79.5 %. Among the 1371 viral peptides detected, 35 peptides with the most intense signals in mass spectrometry were selected, representing a subset of 13 viral proteins. Their relevance as potential candidate markers for virus detection by targeted mass spectrometry is discussed. This report should assist the rapid development of mass spectrometry-based tests to detect a pathogen of increasing concern.     

Use of atmospheric pressure ionization mass spectrometry in enantioselective liquid chromatography

Recent advances in mass spectrometry have rendered it an attractive and versatile tool in industrial and academic research laboratories. As a part of this rapid growth, a considerable body of literature has been devoted to the application of mass spectrometry in studies involving enantioselectivity, molecular recognition, and supramolecular chemistry. In concert with separation techniques such as capillary electrophoresis and liquid chromatography, mass spectrometry allows rapid characterization of a large array of molecules in complex mixtures. A majority of these findings have been made possible by the introduction of 'soft-ionization' techniques such as electrospray ionization interface. Other techniques such as atmospheric pressure chemical ionization mass spectrometry have been widely used as a rugged interface for quantitative liquid chromatography-mass spectrometry. Herein, we present a brief overview of the above techniques accompanied with several examples of enantioselective capillary electrophoresis- and liquid chromatography-mass spectrometry in drug discovery and development. Although the emphasis of this article is on quantitative enantiomeric chromatography-mass spectrometry, we envisage that similar strategies are adaptable in qualitative studies.     

Identification of proteins in cell-free extracts using liquid chromatography-electrospray ionization mass spectrometry

A rapid method for the identification and characterization of proteins in bacterial cell-free extracts has been developed using directly combined liquid chromatography-electrospray mass spectrometry. The usefulness of this technique is demonstrated for monitoring the expression and chemical modification of phosphoenolpyruvate-sugar phosphotransferase system (PTS) proteins from E. coli with molecular masses ranging from 9-65 kDa. The technique is characterized by minimal sample preparation, remarkable mass accuracy and resolution, reproducibility and the ability, unlike gel electrophoresis, to directly identify posttranslational modifications. The advantages of this technique over analogous matrix-assisted laser desorption ionization mass spectrometry approaches and its potential as a standard tool in the biomolecular research laboratory are discussed.     

Ion mobility–mass spectrometry for structural proteomics

Ion mobility coupled to mass spectrometry has been an important tool in the fields of chemical physics and analytical chemistry for decades, but its potential for interrogating the structure of proteins and multiprotein complexes has only recently begun to be realized. Today, ion mobility–mass spectrometry is often applied to the structural elucidation of protein assemblies that have failed high-throughput crystallization or NMR spectroscopy screens. Here, we highlight the technology, approaches and data that have led to this dramatic shift in use, including emerging trends such as the integration of ion mobility–mass spectrometry data with more classical (e.g., ‘bottom-up’) proteomics approaches for the rapid structural characterization of protein networks.     

Integration of surface plasmon resonance with mass spectrometry: automated ligand fishing and sample preparation for MALDI MS using a Biacore 3000 biosensor.

Integrating surface plasmon resonance analysis with mass spectrometry allows detection and characterization of molecular interactions to be complemented with identification of interaction partners. We have developed a procedure for Biacore 3000 that automatically performs all steps from ligand fishing and recovery to sample preparation for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry including on-target digestion. In the model system used in this study a signal transduction protein, calmodulin, was selectively captured from brain extract by one of its interaction partners immobilized on a sensor chip. The bound material was eluted, deposited directly onto a MALDI target, and analyzed by mass spectrometry both as an intact protein and after on-target tryptic digestion. The procedure with direct deposition of recovered material on the MALDI target reduces sample losses and, in combination with automatic sample processing, increases the throughput of surface plasmon resonance mass spectrometry analysis.     

Enrichment of low-molecular-weight proteins from biofluids for biomarker discovery

The dramatic progress in mass spectrometry-based methods of protein identification has triggered a new quest for disease-associated biomarkers. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and its variant surface-enhanced laser desorption/ionization mass spectrometry, provide effective means to explore the less studied information slice of the human serum proteome -- low-molecular-weight proteins and peptides. These low-molecular-weight proteins and peptides are promising for the detection of important biomarkers. Due to the significant experimental problems imposed by high-abundance and high-molecular-weight proteins, it is important to effectively remove these species prior to mass spectrometry analysis of the low-molecular-weight serum and plasma proteomes. In this review, the advantages afforded by recently introduced methods for prefractionation of serum, as they pertain to the detection and identification of biomarkers, will be discussed.