2026-10-12T10:32:35Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33986029 2026-09-24T14:07:49Z category_1 category_4 category_14 category_873 category_734 category_811 category_69 category_135 portal_63 item_type_3 month_year_09_2026

IsoSwap: A Toeplitz Operator Framework for Isotope Transformations in Mass Spectrometry Frédérique Vilenne (19488819) Piotr Prostko (18624291) Dirk Valkenborg (702591) Biophysics Biochemistry Molecular Biology Chemical Sciences not elsewhere classified Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Inorganic Chemistry Computational Biology supports gpu acceleration representing isotopic profiles modeling leaving groups formulation directly yields bound holo forms algebraically transparent method modified elemental formula aggregated isotope probabilities achieve high accuracy experimental mass spectrum transforming isotope distributions toeplitz operator framework isotope distributions mass accuracy toeplitz matrices modified oligonucleotides isotope transformations based framework mass spectrometry specific adaptations specialized handling simulated phosphorothioate recursive expansions product expansions poor adaptability polyisotopic elements point precision operators interconvert neutron count naturally extends limited scalability introduce hankel function methods existing algorithms direct recomputation chemical modifications biomolecule identification approximately 5 6 times 1 ppm Accurate prediction of isotope distributions is essential for biomolecule identification and quantitation in mass spectrometry. Existing algorithms, such as recursive expansions or generating-function methods, achieve high accuracy but suffer from limited scalability, specialized handling of polyisotopic elements such as sulfur, and poor adaptability to chemical modifications. We present IsoSwap, a convolution-based framework that reformulates isotope distribution calculations as structured linear algebra operations. By representing isotopic profiles as discrete probability vectors indexed by neutron count, we express convolution as outer-product expansions and introduce Hankel and Toeplitz matrices. This formulation directly yields both aggregated isotope probabilities and centroid masses, and naturally extends to deconvolution for modeling leaving groups. IsoSwap computes complete isotopic envelopes in milliseconds, supports GPU acceleration, and generalizes to higher-order convolutions without element-specific adaptations. On simulated phosphorothioate-modified oligonucleotides, IsoSwap reproduces distributions computed directly from the modified elemental formula to floating-point precision, at approximately 5.6 times the speed of direct recomputation. Applied to an experimental mass spectrum of myoglobin, the operators interconvert the apo and heme-bound holo forms in both directions, with centroid-mass accuracy below 1 ppm. This provides a scalable, algebraically transparent method for predicting and transforming isotope distributions. 2026-09-24T00:00:00Z Dataset Dataset 10.1021/acs.analchem.6c01495.s001 https://figshare.com/articles/dataset/IsoSwap_A_Toeplitz_Operator_Framework_for_Isotope_Transformations_in_Mass_Spectrometry/33986029 CC BY-NC 4.0