Mass Spectrometry
Online ISSN : 2186-5116
Print ISSN : 2187-137X
ISSN-L : 2186-5116
Current issue
Showing 1-5 articles out of 5 articles from the selected issue
Original Article
  • Kosuke Ogata, Chih-Hsiang Chang, Yasushi Ishihama
    2021 Volume 10 Issue 1 Pages A0093
    Published: January 30, 2021
    Released: January 30, 2021
    [Advance publication] Released: December 11, 2020
    Supplementary material

    The insertion of ion mobility spectrometry (IMS) between LC and MS can improve peptide identification in both proteomics and phosphoproteomics by providing structural information that is complementary to LC and MS, because IMS separates ions on the basis of differences in their shapes and charge states. However, it is necessary to know how phosphate groups affect the peptide collision cross sections (CCS) in order to accurately predict phosphopeptide CCS values and to maximize the usefulness of IMS. In this work, we systematically characterized the CCS values of 4,433 pairs of mono-phosphopeptide and corresponding unphosphorylated peptide ions using trapped ion mobility spectrometry (TIMS). Nearly one-third of the mono-phosphopeptide ions evaluated here showed smaller CCS values than their unphosphorylated counterparts, even though phosphorylation results in a mass increase of 80 Da. Significant changes of CCS upon phosphorylation occurred mainly in structurally extended peptides with large numbers of basic groups, possibly reflecting intramolecular interactions between phosphate and basic groups.

  • Evgeny Zhvansky, Anatoly Sorokin, Vsevolod Shurkhay, Denis Zavorotnyuk ...
    2021 Volume 10 Issue 1 Pages A0094
    Published: March 13, 2021
    Released: March 13, 2021
    [Advance publication] Released: January 22, 2021
    Supplementary material

    Recently developed methods of ambient ionization allow the collection of mass spectrometric datasets for biological and medical applications at an unprecedented pace. One of the areas that could employ such analysis is neurosurgery. The fast in situ identification of dissected tissues could assist the neurosurgery procedure. In this paper tumor tissues of astrocytoma and glioblastoma are compared. The vast majority of the data representation methods are hard to use, as the number of features is high and the amount of samples is limited. Furthermore, the ratio of features and samples number restricts the use of many machine learning methods. The number of features could be reduced through feature selection algorithms or dimensionality reduction methods. Different algorithms of dimensionality reduction are considered along with the traditional noise thresholding for the mass spectra. From our analysis, the Isomap algorithm appears to be the most effective dimensionality reduction algorithm for negative mode, whereas the positive mode could be processed with a simple noise reduction by a threshold. Also, negative and positive mode correspond to different sample properties: negative mode is responsible for the inner variability and the details of the sample, whereas positive mode describes measurement in general.

  • Hiromori Murashima, Akimasa Fujihara
    2021 Volume 10 Issue 1 Pages A0096
    Published: June 10, 2021
    Released: June 10, 2021
    [Advance publication] Released: April 28, 2021

    The gas-phase adsorption of N2 on protonated serine (Ser, C3H7NO3), threonine (Thr, C4H9NO3), glycine (Gly, C2H5NO2), and 2-aminoethanol (C2H7NO) was investigated using a tandem mass spectrometer equipped with an electrospray ionization source and a cold ion trap. N2 molecules were adsorbed on the free X–H (X=O and N) groups of protonated molecules. Gas-phase N2 adsorption-mass spectrometry detected the presence of free X–H groups in the molecular structures, and was applied to the structural elucidation of small molecules. When the 93 structures with an elemental composition of C3H7NO3 were filtered using the gas-phase N2 adsorption-mass spectrometry results for Ser, the number of possible molecular structures was reduced to 8 via the quantification of the X–H groups. Restricting and minimizing the number of possible candidates were effective steps in the structural elucidation process. Gas-phase N2 adsorption-mass spectrometry combined with mass spectrometry-based techniques has the potential for being useful for elucidating the molecular structures of a variety of molecules.

  • Kanako Inoue, Akimasa Fujihara
    2021 Volume 10 Issue 1 Pages A0097
    Published: September 07, 2021
    Released: September 07, 2021
    [Advance publication] Released: July 20, 2021

    The enantioselectivity of tryptophan (Trp) for amino acids, such as alanine (Ala), valine (Val), and serine (Ser), was investigated using ultraviolet (UV) photoexcitation and tandem mass spectrometry. Product ion spectra of cold gas-phase amino acid enantiomers that were hydrogen-bonded to Na+(L-Trp) were measured using a variable-wavelength UV laser and a tandem mass spectrometer equipped with an electrospray ionization source and a cold ion trap. Na+(L-Trp), formed via amino acid detachment, and the elimination of CO2 from the clusters were observed in the product ion spectra. For photoexcitation at 265 nm, the relative abundance of Na+(L-Trp) compared to that of the precursor ion observed in the product ion spectrum of heterochiral Na+(L-Trp)(D-Ala) was larger than that observed in the product ion spectrum of homochiral Na+(L-Trp)(L-Ala). A difference between the Val enantiomers in the relative abundance of the precursor and product ions was observed in the case of photoexcitation at 272 nm. The elimination of CO2 was not observed for L-Ser for the 285 nm photoexcitation, which was the main reaction pathway for D-Ser. Photoexcited Trp chiral recognition was applied to identify and quantify the amino acid enantiomers in solution. Ala, Val, and Ser enantiomers in solution were quantified from their relative abundances in single product ion spectra measured using photoexcitation at 265, 272, and 285 nm, respectively, for hydrogen-bonded Trp within the clusters.