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A detailed experimental characterization on the ion storage biases in an ion funnel trap, related to ion structure, charge state and RF voltage applied to the ion funnel trap, is reported by using both cytochrome C and ubiquitin samples. It was first observed experimentally that an unavoidable ion overflow would occur when the incoming ions exceeded the capacity of ion funnel trap. The conformers with extended structures would lose preferentially in the ion overflow process. Accordingly, a significant structural bias in the ion mobility spectrometry/time of flight mass spectrometry (IMS-TOF MS) spectrum was created, as the peak intensities for conformers with compact structures and extended structures would continuously increase and decrease, respectively, when the ion overflow time of the ion funnel trap was increased. Furthermore, the experimental results also showed that the effect of this ion structural bias was more significant when the RF voltage applied to the ion funnel trap was increased. In addition, an ion charge state bias in the ion funnel trap was also observed. The effect of the ion structural bias depends significantly on the specific charge state of the ions. For a given analyte, its lower charge state ions show a greater sensitivity to the ion structural bias than the higher charge state ones under the same ion funnel trap operating conditions. Therefore, it is extremely important to set a reasonable operation condition for the ion funnel trap to avoid ion storage biases in IMS-TOF MS. [Display omitted] • An ion storage bias in the ion funnel trap of an IMS-QTOF MS was observed. • Ion storage bias was proved to be related to ion structure, charge state and so on. • The method to eliminate the ion storage bias in ion funnel trap was reported. • The optimum operation condition for the ion funnel trap was reported. [ABSTRACT FROM AUTHOR]

A high-performance standalone planar field asymmetric waveform ion mobility spectrometry (p-FAIMS) system with a deconvolution algorithm (two-step particle swarm optimization algorithm, TSPSO) for overlapping peaks was developed to effectively detect chemical warfare agents (CWAs). Four CWA simulants were applied in this study to systemically evaluate the performance of the standalone p-FAIMS system. The experimental results showed that each CWA simulant in the mixture can be positively identified by carefully comparing the compensation voltage (CV) value of each peak in the FAIMS spectra for the mixture to the ones in the spectra acquired by using the same FAIMS system for the pure CWA simulant standards. The FAIMS spectrum of the CWA simulant mixture might consist of multiple overlapping peaks, which would be difficult to accurately determine the CV value for each CWA simulant peak. This problem has been effectively resolved in this study by deconvoluting the overlapping peaks via the TSPSO algorithm. As the effective peak deconvolution via TSPSO requires the degree of overlap between each FAIMS peak to be lower than a specific value, the flow rate of FAIMS carrier gas was decreased to further improve the resolution of the p-FAIMS system. After the accurate deconvolution, the resolution of original FAIMS spectrum can also be enhanced to achieve baseline separation by using TSPSO algorithm to narrow the peak width of each peak. The experimental results in this study demonstrated the possibility of using TSPSO algorithm to achieve high-resolution on a typically low-resolution standalone FAIMS. The concept in this study can potentially be applied to any low-resolution instruments to achieve high-resolution results. [Display omitted] • A high-performance standalone FAIMS system was developed in this study. • The chemical warfare agent mixtures were effectively analyzed by using FAIMS. • The overlaid peaks in FAIMS spectra can be effectively deconvoluted via TSPSO algorithm. • The FAIMS spectra can be enhanced to achieve baseline separation using TSPSO algorithm. [ABSTRACT FROM AUTHOR]

It has been confirmed that endogenous glycopeptide plays an important role in a variety of pathological and physiological processes. However, direct analysis of endogenous glycopeptide is still a great challenge owing to the low abundance of endogenous glycopeptides and the presence of a large number of interfering substances such as large-sized proteins and heteropeptides in complex biological sample. Herein, we reported a novel bowl-like mesoporous polydopamine nanoparticle modified by carrageenan (denoted as MPDA@PEI@CA) with strong hydrophilicity and size-exclusion effect for high specificity enrichment of endogenous glycopeptides. Thanks to the suitable pore channel structure as well as strong hydrophilic surface, the as-prepared MPDA@PEI@CA nanoparticles exhibited prominent performance in enrichment of N-linked glycopeptide with ultrahigh selectivity (1:5000 M ratio of horseradish peroxidase (HRP) digests/bovine serum albumin (BSA) digests), low detection limit (5 fmol μL−1), outstanding size-exclusion ability (1:1000 mass of HRP/BSA), and unique reusability (five times). 125 N-glycosylation sites of 134 glycopeptides from 65 glycoproteins were identified from 2 μL sample of human serum treated with the MPDA@PEI@CA nanoparticles, which manifested the ability to enrich endogenous N-linked glycopeptides from complex biological samples. These results indicated that the bowl-like MPDA@PEI@CA nanoparticles with novel structure prepared in this work had great potential for glycopeptidome analysis. [Display omitted] • A bowl-like mesoporous MPDA@PEI@CA composite was fabricated. • The MPDA@PEI@CA had suitable mesoporous structure and strong hydrophilicity. • The MPDA@PEI@CA exhibited ultrahigh selectivity for glycopeptides enrichment. • The MPDA@PEI@CA presented the ability to enrich glycopeptides from human serum. [ABSTRACT FROM AUTHOR]

Glycosylated proteins are an essential class of molecules playing critical roles in complex biological systems. Understanding their biological functions remains extremely difficult due to the extremely broad compositions and structure variations of glycans. Although the combination of ion mobility spectrometry and mass spectrometry (IMS-MS) has become a promising technique in glycan structure characterization and composition identification, the insufficient resolving power of most IMS-MS instruments has limited its utility in performing the comprehensive structure characterization of glycans. To mitigate the low IMS resolving power, metal ion incorporation has been employed to enhance the separation of isomeric glycans. Here, we present a systematic investigation of many different glycan-metal ion complexes in an attempt to optimize the IMS separation of different isomeric glycans. By selecting optimum glycan-metal ion complexes, partial IMS separation was realized for all the 21 isomeric glycan pairs used in the experimental study. Baseline IMS separation was achieved for 76% of these isomeric glycan pairs. The best IMS separation of isomeric glycans was achieved in some cases by incorporating multiple ions with a glycan, such as the complex [glycan + Ca + Cl]+. In addition, the well-known IMS-MS measurement trendlines, often used to identify specific compound classes, were preserved for glycans even for all the 270 glycan-metal ion complexes observed in IMS-MS spectra. Image 1 • The structure and conformational diversity of glycans were greatly changed by the incorporation of metal ions in gas phase. • The optimum separation of glycan isomers was achieved in some cases by incorporating multiple ions with a glycan. • Baseline IMS separation was realized for 76% of all isomeric glycan pairs used in the experimental study. • The well-known IMS-MS measurement trendlines were preserved for all the 270 glycan-metal ion complexes. [ABSTRACT FROM AUTHOR]