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Four-dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF.
Mun, Dong-Gi; Budhraja, Rohit; Bhat, Firdous A; Zenka, Roman M; Johnson, Kenneth L; Moghekar, Abhay; Pandey, Akhilesh.
Afiliación
  • Mun DG; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
  • Budhraja R; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
  • Bhat FA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
  • Zenka RM; Proteomics Core, Mayo Clinic, Rochester, Minnesota, USA.
  • Johnson KL; Proteomics Core, Mayo Clinic, Rochester, Minnesota, USA.
  • Moghekar A; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
  • Pandey A; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
Proteomics ; 23(10): e2200507, 2023 05.
Article en En | MEDLINE | ID: mdl-36752121
A quadrupole time-of-flight mass spectrometer coupled with a trapped ion mobility spectrometry (timsTOF) operated in parallel accumulation-serial fragmentation (PASEF) mode has recently emerged as a platform capable of providing four-dimensional (4D) features comprising of elution time, collision cross section (CCS), mass-to-charge ratio, and intensity of peptides. The PASEF mode provides ∼100% ion sampling efficiency both in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes without sacrificing sensitivity. In addition, targeted measurements using PASEF integrated parallel reaction monitoring (PRM) mode have also been described. However, only limited number of studies have used timsTOF for analysis of clinical samples. Although Orbitrap mass spectrometers have been used for biomarker discovery from cerebrospinal fluid (CSF) in a variety of neurological diseases, these Orbitrap-derived datasets cannot readily be applied for driving experiments on timsTOF mass spectrometers. We generated a catalog of peptides and proteins in human CSF in DDA mode on a timsTOF mass spectrometer and used these data to build a spectral library. This strategy allowed us to use elution times and ion mobility values from the spectral library to design PRM experiments for quantifying previously discovered biomarkers from CSF samples in Alzheimer's disease. When the same samples were analyzed using a DIA approach combined with a spectral library search, a higher number of proteins were identified than in a library-free approach. Overall, we have established a spectral library of CSF as a resource and demonstrated its utility for PRM and DIA studies, which should facilitate studies of neurological disorders.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteómica / Espectrometría de Movilidad Iónica Límite: Humans Idioma: En Revista: Proteomics Asunto de la revista: BIOQUIMICA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Alemania
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteómica / Espectrometría de Movilidad Iónica Límite: Humans Idioma: En Revista: Proteomics Asunto de la revista: BIOQUIMICA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Alemania