Positive and negative‐mode laser desorption/ionization‐mass spectrometry (LDI‐MS) for the detection of indigoids in archaeological purple

Laser‐based ionization techniques have demonstrated to be a valuable analytical tool to study organic pigments by mass spectrometric analyses. Though laser‐based ionization techniques have identified several natural and synthetic organic dyes and pigments, they have never been used in the characterization of purple. In this work, positive and negative‐mode laser desorption/ionization mass spectrometry (LDI‐MS) was used for the first time to detect indigoids in shellfish purple. The method was used to study organic residues collected from archaeological ceramic fragments that were known to contain purple, as determined by a classical high‐performance liquid chromatography‐based procedure. LDI‐MS provides a mass spectral fingerprint of shellfish purple, and it was found to be a rapid and successful tool for the identification of purple. In addition, a comparison between positive and negative mode ionization highlighted the complementarity of the two ionization modes. On the one hand, the negative‐ion mode LDI‐MS showed a better selectivity and sensitivity to brominated molecules, such as 6,6'‐dibromoindigo, 6‐monobromoindigo, 6,6'‐dibromoindirubin, 6‐ and 6’‐monobromoindirubin, thanks to their electronegativity, and produced simpler mass spectra. On the other hand, negative‐ion mode LDI‐MS was found to have a lower sensitivity to non‐brominated compounds, such as indigo and indirubin, whose presence can be established in any case by collecting the complementary positive‐ion LDI mass spectrum. Copyright © 2013 John Wiley & Sons, Ltd.     

Comprehensive characterization of natural organic matter by MALDI- and ESI-Fourier transform ion cyclotron resonance mass spectrometry

Natural organic matter (NOM) is a complex and non-uniform mixture of organic compounds which plays an important role in environmental processes. Due to the complexity, it is challenging to obtain fully detailed structural information about NOM. Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) has been demonstrated to be a powerful tool for providing molecular information about NOM, multiple ionization methods are needed for comprehensive characterization of NOM at the molecular level considering the ionizing selectivity of different ionization methods. This paper reports the first use of matrix assisted laser desorption/ionization (MALDI) method coupled with FT-ICR-MS for molecular characterization of NOM within a mass range of 200–800 Da. The mass spectral data obtained by MALDI were systematically compared with data generated by electrospray ionization (ESI). It showed that complementary molecular information about NOM which could not be detected by ESI, were provided by MALDI. More unsaturated and aromatic constituents of NOM with lower O/C ratio (O/C ratio < 0.5) were preferentially ionized in MALDI negative mode, whereas more polar constituents of NOM with higher O/C ratio were preferentially ionized in ESI negative mode. Molecular anions of NOM appearing at even m/z in MALDI negative ion mode were detected. The results show that NOM molecules with aromatic structures, moderate O/C ratio (0.7 > O/C ratio > 0.25) and lower H/C ratio were liable to form molecular anions at even m/z, whereas those with higher H/C ratio are more likely to form deprotonated ions at odd m/z. It is speculated that almost half of the NOM molecules identified by MALDI may be aromatic or condensed aromatic compounds with special groups which are liable to absorb electron from other molecules to generate free radical anions during MALDI ionization.     

The application of electrospray ionization coupled to ultrahigh resolution mass spectrometry for the molecular characterization of natural organic matter

Mass spectrometry has recently played a key role in the understanding of natural organic matter (NOM) by providing molecular-level details about its composition. NOM, a complex assemblage of organic molecules present in natural waters and soils/sediments, has the ability to bind and transport anthropogenic materials. An improved understanding of its composition is crucial in order to understand how pollutants interact with NOM and how NOM cycles through global carbon cycles. In the past, low-resolution (>3000) mass analyzers have offered some insights into the structure of NOM, but emerging ultrahigh resolution (>200,000) techniques such as electrospray ionization (ESI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) have significantly advanced our knowledge of NOM chemistry. Here, a review of the recent literature on the advancements of NOM characterization and the applications of mass spectrometry to this central task is presented. Various methods for the analysis and display of the extremely complex mass spectra, such as the van Krevelen diagram and Kendrick mass defect analysis, are discussed. We also review tandem mass spectrometry techniques employed to gain structural information about NOM components. Finally, we show how ESI-FT-ICR-MS has been applied to examine specific issues that are important to the NOM scientific community, such as NOM reactivity, transport and fate, degradation, and existence of components, which are indicators of NOM origin. In general, ultrahigh resolution provided by FT-ICR-MS is essential for the complete separation of the thousands of peaks present in the complex NOM mixture and will clearly lead to additional future advancements in the areas of aquatic, soil, and analytical chemistry.     

The carbon versus mass diagram to visualize and exploit FTICR‐MS data of natural organic matter

A two‐dimensional diagram is proposed, in which the carbon number of each formula is plotted against its nominal mass, to visualize large sets of molecular formula data that can be derived from data generated by ultrahigh‐resolution Fourier transform ion cyclotron resonance‐MS. In such a carbon versus mass (CvM) diagram, each formula (C_cH_hO_o) is unambiguously described by c, its (nominal) mass and the parameter i = c + o. Calculations of chemically allowable formulas illustrate that organic molecules occupy only certain spaces in such a diagram. The extension of these spaces increases with molecular mass in x‐direction (hydrogenation) and y‐direction (oxygenation). The data sets of molecules determined in natural organic matter(NOM) occupy only a certain range of the allowable space. The intensity of the mass spectrometric signals can be included as the third dimension into a CvM diagram. Separate CvM diagrams can be plotted for NOM molecules that include different heteroatoms. The benefits of the CvM diagram are illustrated by application onto data sets of fulvic acids from riverine and marine origin, of secondary organic aerosol, including organosulfates and organonitrates, as well as of ozonation of fulvic acids. The CvM diagram is a useful tool to visualize the elemental regularities in NOM isolates as well as the differences between isolates. It may also be applicable to large sets of molecular formula data generated in other disciplines such as petroleum biogeochemistry or metabolomics. Copyright © 2010 John Wiley & Sons, Ltd.     

Application of high‐resolution ESI and MALDI mass spectrometry to metabolite profiling of small interfering RNA duplex

We investigated the application of a high‐resolution Orbitrap mass spectrometer equipped with an electrospray ionization (ESI) source and a matrix‐assisted laser desorption/ionization‐time‐of‐flight (MALDI‐TOF) mass spectrometer to the metabolite profiling of a model small interfering RNA (siRNA) duplex TSR#34 and compared their functions and capabilities. TSR#34 duplex was incubated in human serum in vitro, and the duplex and its metabolites were then purified by ion exchange chromatography in order to remove the biological matrices. The fraction containing the siRNA duplex and its metabolites was collected and desalted and then subjected to high‐performance liquid chromatography (HPLC) equipped with a reversed phase column. The siRNA and its metabolites were separated into single strands by elevated chromatographic temperature and analyzed using the ESI‐Orbitrap or the MALDI‐TOF mass spectrometer. Using this method, the 5' and/or 3' truncated metabolites of each strand were detected in the human serum samples. The ESI‐Orbitrap mass spectrometer enabled differentiation between two possible RNA‐based sequences, a monoisotopic molecular mass difference which was less than 2 Da, with an intrinsic mass resolving power. In‐source decay (ISD) analysis using a MALDI‐TOF mass spectrometer allowed the sequencing of the RNA metabolite with characteristic fragment ions, using 2,4‐dihydroxyacetophenone (2,4‐DHAP) as a matrix. The ESI‐Orbitrap mass spectrometer provided the highest mass accuracy and the benefit of on‐line coupling with HPLC for metabolite profiling. Meanwhile, the MALDI‐TOF mass spectrometer, in combination with 2,4‐DHAP, has the potential for the sequencing of RNA by ISD analysis. The combined use of these methods will be beneficial to characterize the metabolites of therapeutic siRNA compounds. Copyright © 2012 John Wiley & Sons, Ltd.     

Mass spectrometric analysis of low molecular mass polyesters by laser desorption/ionization on porous silicon

A low molecular mass polyester was analyzed by desorption/ionization on porous silicon (DIOS) mass spectrometry. The results were compared with those of matrix-assisted laser desorption ionization (MALDI) mass spectrometry using matrixes of alpha-cyano-4-hydroxycinnamic acid (CHCA) and 10,15,20-tetrakis(pentafluorophenyl)porphyrin (F20TPP). The CHCA matrix was not suitable for characterization of low molecular mass components of the polyester because the matrix-related ions interfered with the component ions. On the other hand, the F20TPP matrix showed no interference because no matrix-related ions appeared below m/z 822. However, the solvent selection for determining optimal conditions of sample preparation was limited, because F20TPP does not dissolve readily in any of the available organic solvents. In the DIOS spectra, the polymer ions were observed at high sensitivity without a contaminating ion. No matrix is needed for DIOS spectra of low molecular mass polyesters, facilitating sample preparation and selectivity of a precursor ion in post-source decay measurements.     

Analysis of lipids with desorption atmospheric pressure photoionization‐mass spectrometry (DAPPI‐MS) and desorption electrospray ionization‐mass spectrometry (DESI‐MS)

In this article, the effect of spray solvent on the analysis of selected lipids including fatty acids, fat‐soluble vitamins, triacylglycerols, steroids, phospholipids, and sphingolipids has been studied by two different ambient mass spectrometry (MS) methods, desorption electrospray ionization‐MS (DESI‐MS) and desorption atmospheric pressure photoionization‐MS (DAPPI‐MS). The ionization of the lipids with DESI and DAPPI was strongly dependent on the spray solvent. In most cases, the lipids were detected as protonated or deprotonated molecules; however, other ions were also formed, such as adduct ions (in DESI), [M‐H]⁺ ions (in DESI and DAPPI), radical ions (in DAPPI), and abundant oxidation products (in DESI and DAPPI). DAPPI provided efficient desorption and ionization for neutral and less polar as well as for ionic lipids but caused extensive fragmentation for larger and more labile compounds because of a thermal desorption process. DESI was more suitable for the analysis of the large and labile lipids, but the ionization efficiency for less polar lipids was poor. Both methods were successfully applied to the direct analysis of lipids from pharmaceutical and food products. Although DESI and DAPPI provide efficient analysis of lipids, the multiple and largely unpredictable ionization reactions may set challenges for routine lipid analysis with these methods. Copyright © 2012 John Wiley & Sons, Ltd.     

The improved performance of MALDI‐TOF MS on the analysis of herbal saponins by using DHB‐GO composite matrix

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) is an excellent analytical technique for rapid analysis of a variety of molecules with straightforward sample pretreatment. The performance of MALDI‐TOF MS is largely dependent on matrix type, and the development of novel MALDI matrices has aroused wide interest. Herein, we devoted to seek more robust MALDI matrix for herbal saponins than previous reported, and ginsenoside Rb1, Re, and notoginsenoside R1 were used as model saponins. At the beginning of the present study, 2,5‐dihydroxybenzoic acid (DHB) was found to provide the highest intensity for saponins in four conventional MALDI matrices, yet the heterogeneous cocrystallization of DHB with analytes made signal acquisition somewhat “hit and miss.” Then, graphene oxide (GO) was proposed as an auxiliary matrix to improve the uniformity of DHB crystallization due to its monolayer structure and good dispersion, which could result in much better shot‐to‐shot and spot‐to‐spot reproducibility of saponin analysis. The satisfactory precision further demonstrated that minute quantities of GO (0.1 μg/spot) could greatly reduce the risk of instrument contamination caused by GO detachment from the MALDI target plate under vacuum. More importantly, the sensitivity and linearity of the standard curve for saponins were improved markedly by DHB‐GO composite matrix. Finally, the application of detecting the Rb1 in complex biological sample was exploited in rat plasma and proved it applicable for pharmacokinetic study quickly. This work not only opens a new field for applications of DHB‐GO in herbal saponin analysis but also offers new ideas for the development of composite matrices to improve MALDI MS performance.     

Charge derivatization by 4-sulfophenyl isothiocyanate enhances peptide sequencing by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

High-sensitivity, rapid identification of proteins in proteomic studies normally uses a combination of one- or two-dimensional electrophoresis together with mass spectrometry. The simplicity and sensitivity of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) have increased its application in recent years. The most common method of 'peptide fingerprinting' often may not provide robust identification. Normally additional sequence information by post-source decay (PSD) MALDI-TOFMS provides additional constraints for database searches to achieve highly confident results. Here we describe a derivatization procedure to facilitate the acquisition of such sequence information. Peptide digests from a skin-expressed protein were modified with 4-sulfophenyl isothiocyanate. The resulting peptides carry a fixed negative charge at the N-terminal end and the resulting PSD spectrum is dominated by C-terminal y-type ions. The sequence information in most cases can be obtained manually or with simple programming tools. Methods of optimizing the procedure and increasing the sensitivity are discussed.     

Stable isotope labeling for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay analysis of ribonucleic acids

Matrix-assisted laser desorption/ionization mass spectrometry is a powerful analytical tool for the structural characterization of oligonucleotides and nucleic acids. Here we report the application of stable isotope labeling for the simplified characterization of ribonucleic acids (RNAs). An (18)O label is incorporated at the 3'-phosphate of oligoribonucleotides during the enzymatic processing of intact RNAs. As implemented, a buffer solution containing a 50 : 50 mixture of H(2)O and (18)O-labeled H(2)O is used during endonuclease digestion. Upon digestion, characteristic doublets representative of the isotopic distribution of oxygen are noted for those products that contain 3'-phosphate groups. This approach is used to distinguish readily endonuclease digestion products from incomplete digestion products and non-specific cleavage products. In addition, RNase digestion products containing the characteristic isotopic doublet can be selected for further characterization by post-source decay (PSD) analysis. PSD products carrying the 3'-phosphate group will appear as a doublet, thereby simplifying fragment ion assignment.     

Fundamental properties of a touchable high‐power pulsed microplasma jet and its application as a desorption/ionization source for ambient mass spectrometry

Plasma‐based ambient desorption/ionization mass spectrometry (ADI–MS) has attracted considerable attention in many fields because of its capacity for direct sample analyses. In this study, a high‐power pulsed microplasma jet (HPPMJ) was developed and investigated as a new plasma desorption/ionization source. In an HPPMJ, a microhollow cathode discharge is generated in a small hole (500 µm in diameter) using a pulsed high‐power supply. This system can realize a maximum power density of 5 × 10⁸ W/cm³. The measured electron number density, excitation temperature and afterglow gas temperature of the HPPMJ were 3.7 × 10¹⁵ cm^‐3, 7000 K at maximum and less than 60 °C, respectively, which demonstrate that the HPPMJ is a high‐energy, high‐density plasma source that is comparable with an argon inductively coupled plasma while maintaining a low gas temperature. The HPPMJ causes no observable damage to the target because of its low gas temperature and electrode configuration; thus, we can apply it directly to human skin. To demonstrate the analytical capacity of ADI–MS using an HPPMJ, the plasma was applied to direct solid sample analysis of the active ingredients in pharmaceutical tablets. Caffeine, acetaminophen, ethenzamide, isopropylantipyrine and ibuprofen were successfully detected. Application to living tissue was also demonstrated, and isopropylantipyrine on a finger was successfully analyzed without damaging the skin. The limits of detection (LODs) for caffeine, isopropylantipyrine and ethenzamide were calculated, and LODs at the picogram level were achieved. These results indicate the applicability of the HPPMJ for high‐sensitivity analysis of materials on a heat‐sensitive surface. Copyright © 2014 John Wiley & Sons, Ltd.     

Analysis of low molecular weight compounds using MALDI‐ and LDI‐TOF‐MS: Direct detection of active pharmaceutical ingredients in different formulations

Matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) is a high throughput, easy to use analytical technique. The simple sample preparation of this technique and its tolerance to the presence of contaminants are among its advantages. In contrast, depending on the matrix used, MALDI can ionize and generates ions in the low m /z range that complicate the interpretation of the spectra of low molecular weight compounds. To address this issue, one can envisage the use of tunable ionic matrices that can reduce the low m /z interferents. In this work, the ionic matrices triethylammonium α‐cyano‐4‐hydroxycinnamate and diisopropylammonium α‐cyano‐4‐hydroxycinnamate were used to directly analyze 14 pharmaceutical drugs in different formulations (coated tablets, noncoated tablets, capsules, and solutions). This methodology enabled the detection of their active compounds with minimum sample preparation, thus providing a straightforward approach for the forensic analysis of pharmaceutical drugs in the quest for detecting counterfeits. LDI‐MS experiments were also performed, and the active ingredient in all of the medicines analyzed were detected. However, MALDI‐MS spectra for the medicines analyzed herein showed less or no fragmentation than LDI‐MS, which makes the analysis easier.     

An approach to analysis of primary amines by a combination of thin‐layer chromatography and matrix‐assisted laser desorption ionization mass spectrometry in conjunction with post‐chromatographic derivatization

On‐spot derivatization has been suggested for the modification of primary amine containing compounds for their analysis by thin‐layer chromatography hyphenated with matrix‐assisted laser desorption ionization mass spectrometry. The proposed approach was based on post‐chromatographic treatment of separated analytes inside the chromatographic zones on the thin‐layer chromatography plates by tris(2,6‐dimethoxyphenyl)methilium reagent. The derivatives, containing permanent positive charge, reveal exceptionally intense peaks of their cationic moieties and high signal/noise ratio in mass spectra recorded directly from the plates. The method was tested on a series of aliphatic, aromatic, and amine‐containing pharmaceuticals.     

基体辅助激光解吸电离飞行时间质谱用于寡糖的分析

将基体辅助激光解吸电离飞行时间质谱这种新兴的质谱方法用于植物中寡糖的分析。比较了不同的样品制备方法和检测方法对分析结果的影响,给出各寡糖样品的分子量分布,单体和端基基团的分子量。     

Normal‐phase high‐performance counter‐current chromatography for the fractionation of dissolved organic matter from a freshwater source

Normal‐phase high‐performance counter‐current chromatography (HPCCC) is used to obtain a preliminary fractionation of components in dissolved organic matter (DOM) from a freshwater source. The HPCCC solvent system involved a normal‐phase approach with water/methanol (1:1) as the lower stationary phase and hexane/ethyl acetate (1:1) as the upper mobile phase. The critical experiment parameters were optimised: revolution speed 1800 rpm and flow rate 0.15 mL/min. Under these conditions 50 μL of a 0.50 mg/mL DOM solution was loaded. The detection wavelength was monitored at 330 nm in order to isolate the main portion of DOM, which includes substances such as carboxyl‐rich alicyclic molecules. By optimising this system it was possible to isolate materials that, according to GC–MS, can be related to molecules with an analogous structural background. Where fraction analysis was not suitable for GC–MS, RP‐HPLC with UV absorbance detection was used, showing unique chromatograms for each fraction at both 210 and 330 nm.     

Fragmentation of organic ions bearing fixed multiple charges observed in MALDI MS

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI TOF MS) was used to analyze a series of synthetic organic ions bearing fixed multiple charges. Despite the multiple intrinsic charges, only singly charged ions were recorded in each case. In addition to the pseudo‐molecular ions formed by counterion adduction, deprotonation and electron capture, a number of fragment ions were also observed. Charge splitting by fragmentation was found to be a viable route for charge reduction leading to the formation of the observed singly charged fragment ions. Unlike multivalent metal ions, organic ions can rearrange and/or fragment during charge reduction. This fragmentation process will evidently complicate the interpretation of the MALDI MS spectrum. Because MALDI MS is usually considered as a soft ionization technique, the fragment ion peaks can easily be erroneously interpreted as impurities. Therefore, the awareness and understanding of the underlying MALDI‐induced fragmentation pathways is essential for a proper interpretation of the corresponding mass spectra. Due to the fragment ions generated during charge reduction, special care should be taken in the MALDI MS analysis of multiply charged ions. In this work, the possible mechanisms by which the organic ions bearing fixed multiple charges fragment are investigated. With an improved understanding of the fragmentation mechanisms, MALDI TOF MS should still be a useful technique for the characterization of organic ions with fixed multiple charges.     

Evaluation of the titanium dioxide approach for MS analysis of phosphopeptides

The affinity of titanium dioxide for phosphate groups has been successfully used for enrichment of phosphopeptides from complex mixtures. This paper reports the relationship between the occurrence of some amino acids and the phospho-specific and nonspecific binding of peptides that occurs during titanium dioxide enrichment. In order to perform a systematic study, two well-characterized peptide mixtures consisting of either 33 or 8 synthetic phosphopeptides and their nonphosphorylated analogs, which differed in charge and hydrophobicity, were synthesized and analyzed by ESI-MS and MALDI-MS. The titanium dioxide procedure was also evaluated for comprehensive detection of phosphopeptides in phosphoproteomics. In summary, our results clearly confirm the high selectivity of titanium dioxide for phosphorylated sequences. Drastically reduced recovery was observed for phosphopeptides with multiple basic amino acids. Nonspecific binding of nonphosphorylated peptides and sample loss of phosphopeptides must also be taken into account.     

Ring‐expansion polymerization of meso‐lactide catalyzed by dibutyltin derivatives

Meso‐Lactide was polymerized in bulk at 60, 80, and 100 °C by means of three different types of catalysts: dibutyltin sulfides (2,2‐dibutyl‐2‐stanna‐1,3‐dithiolane and 2,2′‐dibutyl‐2‐stanna‐1,3‐dithiane), dibutyltin derivatives of substituted catechols (BuCa, CyCa, and BzCa), and dibutyltin derivatives of 2,2′dihydroxybiphenyl (SnBi) and 2,2′‐dihydroxy‐1,1′‐binaphthyl (SnNa). Only the latter two catalysts were active at 60 °C. The architecture of the resulting polylactides depends very much on the structure of the catalyst and on the temperature. At the lowest temperature (60 °C), SnBi and SnNa mainly yielded even‐numbered linear chains, but SnNa also yielded even‐numbered cycles at 100 °C and short reaction times. In contrast, BuCa, CyCa, and BzCa mainly yielded odd‐numbered cycles, although the same catalysts yielded even‐numbered linear chains when benzylalcohol was added. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018 , 56, 749–759     

Laser desorption/ionization mass spectrometry of dye‐sensitized solar cells: identification of the dye‐electrolyte interaction

Dye‐sensitized solar cells (DSCs) have great potential to provide sustainable electricity from sunlight. The photoanode in DSCs consists of a dye‐sensitized metal oxide film deposited on a conductive substrate. This configuration makes the photoanode a perfect sample for laser desorption/ionization mass spectrometry (LDI‐MS). We applied LDI‐MS for the study of molecular interactions between a dye and electrolyte on the surface of a TiO₂ photoanode. We found that a dye containing polyoxyethylene groups forms complexes with alkali metal cations from the electrolyte, while a dye substituted with alkoxy groups does not. Guanidinium ion forms adducts with neither of the two dyes. Copyright © 2015 John Wiley & Sons, Ltd.     

Independent highly sensitive characterization of asparagine deamidation and aspartic acid isomerization by sheathless CZE‐ESI‐MS/MS

Amino acids residues are commonly submitted to various physicochemical modifications occurring at physiological pH and temperature. Post‐translational modifications (PTMs) require comprehensive characterization because of their major influence on protein structure and involvement in numerous in vivo process or signaling. Mass spectrometry (MS) has gradually become an analytical tool of choice to characterize PTMs; however, some modifications are still challenging because of sample faint modification levels or difficulty to separate an intact peptide from modified counterparts before their transfer to the ionization source. Here, we report the implementation of capillary zone electrophoresis coupled to electrospray ionization tandem mass spectrometry (CZE‐ESI‐MS/MS) by the intermediate of a sheathless interfacing for independent and highly sensitive characterization of asparagine deamidation (deaN) and aspartic acid isomerization (isoD). CZE selectivity regarding deaN and isoD was studied extensively using different sets of synthetic peptides based on actual tryptic peptides. Results demonstrated CZE ability to separate the unmodified peptide from modified homologous exhibiting deaN, isoD or both independently with a resolution systematically superior to 1.29. Developed CZE‐ESI‐MS/MS method was applied for the characterization of monoclonal antibodies and complex protein mixture. Conserved CZE selectivity could be demonstrated even for complex samples, and foremost results obtained showed that CZE selectivity is similar regardless of the composition of the peptide. Separation of modified peptides prior to the MS analysis allowed to characterize and estimate modification levels of the sample independently for deaN and isoD even for peptides affected by both modifications and, as a consequence, enables to distinguish the formation of l ‐aspartic acid or d ‐aspartic acid generated from deaN. Separation based on peptide modification allowed, as supported by the ESI efficiency provided by CZE‐ESI‐MS/MS properties, and enabled to characterize and estimate studied PTMs with an unprecedented sensitivity and proved the relevance of implementing an electrophoretic driven separation for MS‐based peptide analysis. Copyright © 2016 John Wiley & Sons, Ltd.