10papers in this issue.
We are more than happy to see the completion of this special issue in honor of Dr. Jong Shin Yoo’s retirement. Since the establishment of the Korea Society for Mass Spectrometry (KSMS)—the publisher of Mass Spectrometry Letters, he has been one of the core members and served as the second president of KSMS from 2006 to 2007. Dr. Yoo received in Ph.D. degree in Chemistry for Mass Spectrometry from the Michigan State University in 1992, and worked for the Harvard School of Public Health, Boston, USA, as a post-doctoral fellow. Since coming back to Korea in 1993, he has been working on biological mass spectrometry at the Korea Basic Science Institute. He currently holds a joint professorship in Graduate School of Analytical Science and Technology at Chungnam National University. In addition to actively serving as the second president of KSMS, he also served as a president of Korea Human Proteome Organization (KHUPO) in 2008 as well as an international HUPO council member. Dr. Yoo’s research interests have long involved in biological mass spectrometry such as (1) developing bioinformatics tools for N- and O-glycoproteomics, (2) mass spectrometry (MS)-based biomarker development for early diagnosis of cancer, (3) proteogenomic studies for Chromosome-based Human Proteome Project in HUPO, and (4) the instrumental development of 15T-FTICR mass spectrometers. Thirty years of devotions to MS-related research have brought him more than 200 peer-reviewed articles in the leading scientific journals such as Mass Spectrometry Reviews, Scientific Reports, Molecular & Cellular Proteomics, Analytical Chemistry, and Journal of Proteome Research. This special issue contains five excellent articles to honor him. The contributions are from some of the scientists with whom Dr. Yoo has long been collaborating. The topics of the five articles include chromosome-based proteome, N-glycosylation analysis of recombinant proteins, biomarker discovery from serum of scrub typhus patients, MS analysis of low molecular weight collagen, and glycosylation monitoring of antibody therapeutics. We would like to express our sincere gratitude to Dr. Yoo for his effort and devotion for KSMS and look forward to our continued collaborations in the next stage.
As a part of the Chromosome-centric Human Proteome Project (C-HPP), we have developed a few algorithms for accurate identification of missing proteins, alternative splicing variants, single amino acid variants, and characterization of func-tion unannotated proteins. We have found missing proteins, novel and known ASVs, and SAAVs using LC-MS/MS data from human brain and olfactory epithelial tissue, where we validated their existence using synthetic peptides. According to the neXtProt database, the number of missing proteins in chromosome 11 shows a decreasing pattern. The development of genomic and transcriptomic sequencing techniques make the number of protein variants in chromosome 11 tremendously increase. We developed a web solution named as SAAvpedia for identification and function annotation of SAAVs, and the SAAV information is automatically transformed into the neXtProt web page using REST API service. For the 73 uPE1 in hromosome 11, we have studied the function annotaion of CCDC90B (NX_Q9GZT6), SMAP (NX_O00193), and C11orf52 (NX_Q96A22).
Interleukin-4 (IL-4) and IL-13 are cytokines secreted by immune cells. Cytokines induce the proliferation of macro-phages or promote the differentiation of secretory cells. The initiation and progression of allergic inflammatory diseases, such as asthma, are dependent on cytokines acting through related receptor complexes. IL-4 and IL-13 are N-glycoproteins. Glycan structures in glycoproteins play important roles in protein folding, protein stability, enzymatic function, inflammation, and cancer development. Therefore, the glycan structure of IL-4 and IL-13 needs to be elucidated in detail for the development of effective therapies. We report the first attempt to characterize the site-specific N-glycosylation of recombinant IL-4 and IL-13 via liquid chro-matography–tandem mass spectrometry (LC-MS/MS) analysis. The tandem mass spectra of intact N-glycopeptides were identified using the Integrated GlycoProteome Analyzer (I-GPA) platform, which can automatically and rapidly analyze multiple N-glycopep-tides, including their glycan composition and amino acid sequences. The recombinant IL-4 and IL-13 were identified with amino acid sequence coverages of 84% and 96%, respectively. For IL-4, 52 glycoforms on one N-glycosylation site were identified and quantified. In IL-13, 232 N-glycopeptides from three N-glycosylation sites were characterized, with the site Asn52 being the most extensively glycosylated (~80%). The complex glycans were the most abundant glycan on IL-4 and IL-13 (~96% and 91%, respec-tively), and the biantennary glycans were the most abundant in both recombinant IL-4 and IL-13 proteins.
Scrub typhus is an acute febrile disease caused by the pathogenic bacterium Orientia tsutsugamushi, belonging to the Rickettsiaceae family. The shotgun proteomic analysis was performed using the sera of scrub typhus patients to identify the pro-teins having their origin in O. tsutsugamushi. Three different databases approaches were used for the identification of the pro-teomes. We identified the RsmD, an RNA methyltransferase as the commonly detected protein from all three approaches. This protein was not detected in the sera of healthy negative controls. We believe that this protein is a potential biomarker of Orientia tsutsugamushi present in the sera of scrub typhus patients.
Collagen, which accounts for one-third of human protein, is reduced due to human aging, and much attention is focused on making collagen into food to prevent such aging. Gel permeation chromatography with Reflective Index (RI) detec-tion (GPC/RI) was chosen as the most suitable instrument to confirm molecular weight distribution, and we explored the use of this technique for analysis of collagen peptide molecular sizes and distributions. Data reliability was verified by matrix-assisted laser desorption/ionization coupled to time-of-flight (MALDI-TOF) mass spectrometric analysis. The data were considered meaningful for comparative analysis of molecular weight distribution patterns.
The therapeutic antibody drug market has experienced explosive growth as mAbs become the main therapeutic modality for a variety of diseases. Characterization of glycosylation that directly affects the efficacy and safety of therapeutic monoclonal antibodies (mAbs) is critical for therapeutics development, bioprocess system optimization, lot release, and compa-rability evaluation. The LC/MS approach has been widely used to structurally characterize mAbs, and recently attempts have been made to obtain comprehensive information on the primary structure and post-translational modifications (PTMs) of mAbs through intact protein analysis. In this study, we performed state-of-the-art LC/MS based intact protein analysis to readily iden-tify and characterize glycoforms of various mAbs. Different glycoforms of mAbs produced in different expression cell lines includ- ing CHO, SP2/0 and HEK cells were monitored and compared. In addition, the comparability of protein molecular weight, glycoform pattern, and relative abundances of glycoforms between the commercialized trastuzumab biosimilar and the original product was determined in detail using the given platform. Intact mAb analysis allowed us to gain insight into the overall mAb structure, including the complexity and diversity of glycosylation. Furthermore, our analytical platform with high reproducibility is expected to be widely used for biopharmaceutical characterization required at all stages of drug development and manufacturing.
Exosomes have gained the attention of the scientific community because of their role in facilitating intercellular communi-cation, which is critical in disease monitoring and drug delivery research. Exosome research has grown significantly in recent decades, with a focus on the development of various technologies for isolating and characterizing exosomes. Among these efforts is the use of matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS), which offers high-throughput direct analysis while also being cost and time effective. MALDI is used less frequently in exosome research than electrospray ionization due to the diverse popu- lation of extracellular vesicles and the impurity of isolated products, both of which necessitate chromatographic separation prior to MS analysis. However, MALDI-MS is a more appropriate instrument for the analytical approach to patient therapy, given it allows for fast and label-free analysis. There is a huge drive to explore MALDI-MS in exosome research because the technology holds great potential, most notably in biomarker discovery. With methods such as fingerprint analysis, OMICs profiling, and statistical analysis, the search for biomarkers could be much more efficient. In this review, we highlight the potential of MALDI-MS as a tool for investigating exo-somes and some of the possible strategies that can be implemented based on prior research.
Several pretreatment methods have been developed to reduce the inorganic arsenic, which is known to be highly harmful to humans, among various arsenic species present in hijiki and rice. The pretreatment methods were selected and devel-oped as methods that can be non-harmful even after treatment and easily applied. Hijiki was applied by two methods. One was soaking in water at room temperature for various durations and the other was boiling of it in water for a short period of time. Rice was soaked in water with different rice-to-water ratios for various durations. The most effective method that reduced the inorganic arsenic in hijiki was to repeat parboiling for 5 minutes twice, which led to 79% reduction of the inorganic arsenic in it. In the case of rice, soaking for 24 hours at the ratio of 1:5 (rice:water) resulted in 51% reduction of inorganic arsenic in rice.
α-Amanitin and β-amanitin are highly toxic bicyclic octapeptides responsible for the poisoning of poisonous mush-rooms such as Amanita, Galerina, and Lepiota by inhibiting RNA polymerase II, DNA transcription, and protein synthesis. A sensitive, simple, and selective liquid chromatography-high resolution mass spectrometric method using parallel reaction moni-toring mode was developed and validated for the simultaneous determination of α- and β-amanitin in mouse plasma to evaluate the toxicokinetics of α- and β-amanitin in mice. Protein precipitation of 5 μL mouse plasma sample with methanol as sample clean-up procedure and use of negative electrospray ionization resulted in better sensitivity and less matrix effect. The calibra-tion curves for α- and β-amanitin in mouse plasma were linear over the range of 0.5–500 ng/mL. The intra- and inter-day coeffi- cient of variations and accuracies for α- and β-amanitin at four quality control concentrations were 3.1–14.6% and 92.5–115.0%, respectively. The present method was successfully applied to the toxicokinetic study of α- and β-amanitin after an oral adminis-tration of α- and β-amanitin at 1.5 mg/kg dose to male ICR mice.
Many previous studies have focused on revealing the harmfulness of microplastic particles, whereas very few studies have focused on the effects of chemicals, particularly photooxidation product. In this study, products of photodegradation from expanded polystyrene (EPS), compounds produced by photolysis by ultraviolet (UV) light, were investigated. EPS was directly irradiated and photolyzed using a UV lamp, and then the extracted sample was analyzed using high-resolution mass spectrome-try (HRMS). Multiple ionization techniques, including electrospray ionization, atmospheric pressure chemical ionization, and atmospheric pressure photoionization, were used. In total, >300 compounds were observed, among which polystyrene monomer, dimer, and oxidized products were observed. In this work, the data presented clearly demonstrate that it is necessary to identify and monitor oxidized plastic compounds and assess their effect on the environment.