Affiliation:
1. Department of Laboratory Medicine and Pathology Mayo Clinic Rochester Minnesota USA
2. Proteomics Core Mayo Clinic Rochester Minnesota USA
3. Department of Neurology Johns Hopkins University School of Medicine Baltimore Maryland USA
4. Manipal Academy of Higher Education Manipal Karnataka India
5. Center for Individualized Medicine Mayo Clinic Rochester Minnesota USA
Abstract
AbstractA 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.
Funder
National Institute on Aging
National Cancer Institute
Subject
Molecular Biology,Biochemistry
Cited by
2 articles.
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