Peptides derivatized with bicyclic quaternary ammonium ionization tags. Sequencing via tandem mass spectrometry

Quantitative Site-Specific Chemoproteomic Profiling of Protein Lipoylation

Protein lipoylation is an evolutionarily conserved post-translational modification from prokaryotes to eukaryotes. Lipoylation is implicated with several human diseases, including metabolic disorders, cancer, and Alzheimer's disease. While individual lipoylated proteins have been biochemically studied, a strategy for globally quantifying lipoylation with site-specific resolution in proteomes is still lacking. Herein, we developed a butyraldehyde-alkynyl probe to specifically label and enrich lipoylations in complexed biological samples. Combined with a chemoproteomic pipeline using customized tandem enzyme digestions and a biotin enrichment tag with enhanced ionization, we successfully quantified all known lipoylation sites in both Escherichia coli (E. coli) and human proteomes. The strategy enabled us to dissect the dependence of three evolutionarily related lipoylation sites in dihydrolipoamide acetyltransferase (ODP2) in E. coli and evaluated the functional connection between the de novo lipoylation synthetic pathway and the salvage pathway. Our chemoproteomic platform provides a useful tool to monitor the state of lipoylation in proteome samples, which will help decipher molecular mechanisms of lipoylation-related diseases.

Catch, Modify and Analyze: Methods of Chemoselective Modification of Cysteine-Containing Peptides

One effective solution in the analysis of complex mixtures, including protein or cell hydrolysates, is based on chemoselective derivatization of a selected group of compounds by using selective tags to facilitate detection. Another method is based on the capture of the desired compounds by properly designed solid supports, resulting in sample enrichment. Cysteine is one of the rarest amino acids, but at least one cysteine residue is present in more than 91% of human proteins, which clearly confirms its important role in biological systems. Some cysteine-containing peptides may serve as significant molecular biomarkers, which may emerge as key indices in the management of patients with particular diseases. In the current review, we describe recent advances in the development of cysteine-containing peptide modification techniques based on solution and solid phase derivatization and enrichment strategies.

Veni, Vidi, Vici: Immobilized Peptide-Based Conjugates as Tools for Capture, Analysis, and Transformation

Analysis of peptide biomarkers of pathological states of the organism is often a serious challenge, due to a very complex composition of the cell and insufficient sensitivity of the current analytical methods (including mass spectrometry). One of the possible ways to overcome this problem is sample enrichment by capturing the selected components using a specific solid support. Another option is increasing the detectability of the desired compound by its selective tagging. Appropriately modified and immobilized peptides can be used for these purposes. In addition, they find application in studying the specificity and activity of proteolytic enzymes. Immobilized heterocyclic peptide conjugates may serve as metal ligands, to form complexes used as catalysts or analytical markers. In this review, we describe various applications of immobilized peptides, including selective capturing of cysteine-containing peptides, tagging of the carbonyl compounds to increase the sensitivity of their detection, enrichment of biological samples in deoxyfructosylated peptides, and fishing out of tyrosine–containing peptides by the formation of azo bond. Moreover, the use of the one-bead-one-compound peptide library for the analysis of substrate specificity and activity of caspases is described. Furthermore, the evolution of immobilization from the solid support used in peptide synthesis to nanocarriers is presented. Taken together, the examples presented here demonstrate immobilized peptides as a multifunctional tool, which can be successfully used to solve multiple analytical problems.

Analysis of Fragmentation Pathways of Peptide Modified with Quaternary Ammonium and Phosphonium Group as Ionization Enhancers

Peptide modification by a quaternary ammonium group containing a permanent positive charge is a promising method of increasing the ionization efficiency of the analyzed compounds, making ultra-sensitive detection even at the attomolar level possible. Charge-derivatized peptides may undergo both charge remote (ChR) and charge-directed (ChD) fragmentation. A series of model peptide conjugates derivatized with N,N,N-triethyloammonium (TEA), 1-azoniabicyclo[2.2.2]octane (ABCO), 2,4,6-triphenylopyridinium (TPP) and tris(2,4,6-trimetoxyphenylo)phosphonium (TMPP) groups were analyzed by their fragmentation pathways both in collision-induced dissociation (CID) and electron-capture dissociation (ECD) mode. The effect of the fixed-charge tag type and peptide sequence on the fragmentation pathways was investigated. We found that the aspartic acid effect plays a crucial role in the CID fragmentation of TPP and TEA peptide conjugates whereas it was not resolved for the peptides derivatized with the phosphonium group. ECD spectra are mostly dominated by c_n ions. ECD fragmentation of TMPP-modified peptides results in the formation of intense fragments derived from this fixed-charge tag, which may serve as reporter ion.

Selective ESI-MS detection of carbonyl containing compounds by aminooxyacetic acid immobilized on a resin

There are numerous examples of bioactive compounds containing carbonyl groups including modified proteins with oxidation of side chain of amino acid residues to aldehyde/ketone groups which are frequently considered as markers of oxidative stress. The carbonyl unit can be also distinguished as a substructure in many illegal drugs including anabolic steroids as well as cations derivatives. Based on chemoselective formation of oximes by solid phase immobilized hydroxylamine derivatives we proposed the protocol for derivatization and selective detection of carbonylated compounds in human serum albumin hydrolysate as a complex peptide mixture and of testosterone in urine samples. This allowed for the removal of the matrix and the qualitative and quantitative analysis of the derivatized analyte by LC-MS/MS (or LC-MRM). Herein we report the preparation and chemical characterization of a novel, ChemMatrix - based resin functionalized with aminooxyacetic acid (AOA). The hydroxylamine moiety in this resin is combined with a peptide linker (GRG) containing an arginine residue to enhance the ionization efficiency. Application of an isotopically labeled carbonylated peptide ((H-Leu-Val-Thr(O)-Asp-Leu-Thr-Lys [¹³C₆,¹⁵N₂]-OH and testosterone-d₃ allowed us to carry out quantitative analyses of detected compounds. Our method is general and may be applied for analysis of carbonylated compounds in biological samples. Our method based on application of functionalized resin allowed to quantify the level of free testosterone in small sample (0.5 mL) of urine, while the non-derivatized testosterone from urine sample was not detected during direct LC-MRM analysis.

Programmed Formation of HCN Oligomers through Organosulfur Catalysis

An efficient, inexpensive, and reliable synthesis of diaminomaleonitrile (DAMN, 1) is described starting from readily available acetone cyanohydrin as the source of hydrogen cyanide (HCN). Diaminomaleonitrile (DAMN) is known to be an important intermediate in heterocyclic and medicinal chemistry as well as being a possible precursor for the origin of life's hypothesis within prebiotic chemistry. The mechanism of its formation through organosulfur catalysis has been investigated by electrospray ionization mass spectrometry (ESI-MS) using two newly synthesized cationic "marker" molecules as a tool that allows for sensitive detection. As a result, the proposed mechanism of a thiocyanate-mediated synthesis of the HCN tetramer DAMN starting from organic disulfides was confirmed.

Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry

The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.

Application of Safirinium N-Hydroxysuccinimide Esters to Derivatization of Peptides for High-Resolution Mass Spectrometry, Tandem Mass Spectrometry, and Fluorescent Labeling of Bacterial Cells

Mass spectrometry methods are commonly used in the identification of peptides and biomarkers. Due to a relatively low abundance of proteins in biological samples, there is a need for the development of novel derivatization methods that would improve MS detection limits. Hence, novel fluorescent N–hydroxysuccinimide esters of dihydro-[1,2,4]triazolo[4,3-a]pyridin-2-ium carboxylates (Safirinium P dyes) have been synthesized. The obtained compounds, which incorporate quaternary ammonium salt moieties, easily react with aliphatic amine groups of peptides, both in solution and on the solid support; thus, they can be applied for derivatization as ionization enhancers. Safirinium tagging experiments with ubiquitin hydrolysate revealed that the sequence coverage level was high (ca. 80%), and intensities of signals were enhanced up to 8-fold, which proves the applicability of the proposed tags in the bottom–up approach. The obtained results confirmed that the novel compounds enable the detection of trace amounts of peptides, and fixed positive charge within the tags results in high ionization efficiency. Moreover, Safirinium NHS esters have been utilized as imaging agents for fluorescent labeling and the microscopic visualization of living cells such as E. coli Top10 bacterial strain.

Sequential amidation of peptide C-termini for improving fragmentation efficiency

Owing to the poor fragmentation efficiency caused by the lack of a positively charged basic group at the C-termini of peptides, the identification of nontryptic peptides in classical proteomics is known to be less efficient. Particularly, attaching positively charged basic groups to C-termini via chemical derivatizations is known to be able to enhance their fragmentation efficiency. In this study, we introduced a novel strategy, C-termini sequential amidation reaction (CSAR), to improve peptide fragmentation efficiency. By this strategy, C-terminal and side-chain carboxyl groups were firstly amidated by neutral methylamine (MA), and then C-terminal amide bonds were selectively deamidated through peptide amidase while side-chain amide bonds remained unchanged, followed by the secondary amidation of C-termini via basic agmatine (AG). We optimized the amidation reaction conditions to achieve the MA derivatization efficiency of >99% for side-chain carboxyl groups and AG derivatization efficiency of 80% for the hydrolytic C-termini. We applied CSAR strategy to identify bovine serum albumin (BSA) chymotryptic digests, resulting in the increased fragmentation efficiencies (improvement by 9-32%) and charge states (improvement by 39-52%) under single or multiple dissociation modes. The strategy described here might be a promising approach for the identification of peptides that suffered from poor fragmentation efficiency.

Enrichment of Cysteine-Containing Peptide by On-Resin Capturing and Fixed Charge Tag Derivatization for Sensitive ESI-MS Detection

High complexity of cell and tissue proteomes limits the investigation of proteomic biomarkers. Therefore, the methods of enrichment of some chemical groups of peptides including thiopeptides are important tools that may facilitate the proteomic analysis by reducing sample complexity and increasing proteome coverage. Here, we present a new method of cysteine-containing tryptic peptide enrichment using commercially available TentaGel R RAM resin modified by the linker containing the maleimide group, allowing thiol conjugation. The captured tryptic peptides containing lysine residue were then tagged by 2,4,6-triphenylpyrylium salt to form 2,4,6-triphenylpyridinium derivatives, which increases the ionization efficiency during mass spectrometry analysis. This makes it possible to conduct an ultrasensitive analysis of the trace amount of compounds. The proposed strategy was successfully applied in the enrichment of model tryptic podocin peptide and podocin tryptic digest.

Quaternary ammonium isobaric tag for a relative and absolute quantification of peptides

Isobaric labeling quantification of peptides has become a method of choice for mass spectrometry-based proteomics studies. However, despite of wide variety of commercially available isobaric tags, none of the currently available methods offers significant improvement of sensitivity of detection during MS experiment. Recently, many strategies were applied to increase the ionization efficiency of peptides involving chemical modifications introducing quaternary ammonium fixed charge. Here, we present a novel quaternary ammonium-based isobaric tag for relative and absolute quantification of peptides (QAS-iTRAQ 2-plex). Upon collisional activation, the new stable benzylic-type cationic reporter ion is liberated from the tag. Deuterium atoms were used to offset the differential masses of a reporter group. We tested the applicability of QAS-iTRAQ 2-plex reagent on a series of model peptides as well as bovine serum albumin tryptic digest. Obtained results suggest usefulness of this isobaric ionization tag for relative and absolute quantification of peptides.

The unexpected racemization and hydrogen–deuterium exchange of the hydrogen at the α-carbon of proline analogs containing the 5-azoniaspiro[4.4]nonyl-group

Herein, we present an unexpected racemization and the hydrogen–deuterium exchange (HDX) at the α-C atom of the proline derivative under basic aqueous conditions (1% water solution of triethylamine).

New ionization tags based on the structure of the 5-azoniaspiro[4.4]nonyl tag for a sensitive peptide sequencing by mass spectrometry

Quaternary ammonium salts (QAS), both linear and bicyclic, are often utilized to improve the mass spectrometry (MS) analysis of peptides by fixing a permanent positive charge on the analyzed molecule. However, during collision-induced dissociation (CID) experiments, QAS undergo unwanted side reactions-Hofmann elimination as well as a tertiary amine loss- rendering the data interpretation complicated. In this work, we present 2-thia- and 2-oxa-5-azoniaspiro[4.4]nonyl groups as heterocyclic derivatives of the highly stable ionization group, 5-azoniaspiro[4.4]nonyl, for a sensitive peptide analysis by MS. Due to the permanent positive charge, labeled peptides are characterized by enhanced ionization efficiency during electrospray mass spectrometry (ESI-MS) conditions. Moreover, interpretation of the CID fragmentation of labeled peptides is facilitated since a series of generated fragmentation ions enable a complete sequence coverage. Introduction of a heteroatom into the 5-azoniaspiro[4.4]nonyl scaffold allows for liberation of a stable reporter ion which could be used in selected reaction monitoring (SRM)-targeted quantification experiments. Additionally, we synthesized a deuterated analog of the tag for LC-SRM-targeted quantitative analysis. The obtained results indicate the general usefulness of the proposed heterocyclic quaternary ammonium ionization tag for sequencing and quantification of peptides. Graphical abstract New reagents based on the structure of the 5-azoniaspiro[4.4]nonyl tag for peptide analysis by tandem mass spectrometry.

Podocyturia as an early diagnostic marker of preeclampsia: a literature review

CONTEXT

Preeclampsia (PE) is a pregnancy-related disease, and it is a leading cause of maternal and neonatal morbidity and mortality. It is characterized by the new onset of hypertension after 20 weeks of gestation together with signs of organ damage, most commonly the kidneys. The treatment of PE is symptomatic and final intervention requires delivery, regardless of the gestational age of the foetus. Furthermore, PE is a risk factor for developing cardiovascular disease and chronic kidney disease - even many years after the delivery.

OBJECTIVE

Current research of PE has revealed that detection of podocytes in urine (podocyturia) could be a useful method for both confirmation of PE diagnosis and for the prediction of the severity of the disease.

CONCLUSION

The main aim of this review is to summarize the current state of available methods for podocyte detection and to discuss their relevance in clinical practice.

Peptides Labeled with Pyridinium Salts for Sensitive Detection and Sequencing by Electrospray Tandem Mass Spectrometry

Mass spectrometric analysis of trace amounts of peptides may be problematic due to the insufficient ionization efficiency resulting in limited sensitivity. One of the possible ways to overcome this problem is the application of ionization enhancers. Herein we developed new ionization markers based on 2,4,6-triphenylpyridinium and 2,4,6-trimethylpyridinium salts. Using of inexpensive and commercially available pyrylium salt allows selective derivatization of primary amino groups, especially those sterically unhindered, such as ε-amino group of lysine. The 2,4,6-triphenylpyridinium modified peptides generate in MS/MS experiments an abundant protonated 2,4,6-triphenylpyridinium ion. This fragment is a promising reporter ion for the multiple reactions monitoring (MRM) analysis. In addition, the fixed positive charge of the pyridinium group enhances the ionization efficiency. Other advantages of the proposed ionization enhancers are the simplicity of derivatization of peptides and the possibility of convenient incorporation of isotopic labels into derivatized peptides.

Synthesis and mass spectrometry analysis of quaternary cryptando-peptidic conjugates

The bicyclic amines in the form of cryptands, the crown ether analogs, were used in the synthesis of cryptando-peptidic conjugates with simultaneous formation of quaternary ammonium nitrogen moiety. A series of model cryptando-peptidic conjugates at the peptide N-terminus was efficiently prepared by the standard Fmoc solid phase synthesis. Tandem mass spectrometric analysis of the obtained conjugates has shown the specific fragmentation pattern during MS/MS experiment. The obtained cryptandic quaternary ammonium group undergoes the Hofmann elimination during collision-induced dissociation fragmentation followed by the ethoxyl group elimination. The presented quaternization of cryptands by iodoacetylated peptides is relatively easy and compatible with standard solid-phase peptide synthesis. Additionally, the applicability of such peptide derivatives and their isotopologues selectively deuterated at the α-carbon in the quantitative LC-MS analysis was analyzed.