Online-only Table 2 Methodological differences between the studies.
From: Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis
Reference | Brain bank | Protein digestion | Sample clean-up | Mass spectrometer | Pre-fraction technique | Database search engine | Protein database |
|---|---|---|---|---|---|---|---|
Haytural et al. Mol Cell Proteomics, 202014 | Netherlands Brain Bank | Lys-C and Trypsin | Sera Mag SP3 | Q Exactive mass spectrometer (Thermo Scientific) | High resolution iso-electric focusing (72 fractions) | MSGF+ | Ensembl 75 |
Schedin-Weiss et al. (manuscript in preparation) | Netherlands Brain Bank | Trypsin | ZipTip C18 | Q Exactive mass spectrometer (Thermo Scientific) | SCX ion exchange (4 fractions) | Proteome Discoverer | Swiss-Prot |
Bereczki et al. Brain, 20188 | The Brains for Dementia Research | Lys-C and Trypsin | FASP | Q Exactive mass spectrometer (Thermo Scientific) | High resolution iso-electric focusing (72 fractions) | MSGF+ | Swiss-Prot |
Mendonça et al. Neurobiol Dis, 201919 | Human Brain Tissue Bank from Semmelweis University, Budapest | Trypsin | FASP | Q Exactive mass spectrometer (Thermo Scientific) | No | Proteome Discoverer | Swiss-Prot |
Ping et al. Sci Data, 201812 | Emory Alzheimer’s Disease Research Center Brain Bank | Lys-C and Trypsin | Sep-Pak C18 cartridge | Orbitrap Fusion mass spectrometer (Thermo Scientific) | Electrostatic repulsion-hydrophilic interaction chromatography (21 fractions) | Proteome Discoverer | Swiss-Prot TrEMBL |
Johnson et al. Mol Neurodegener, 201810 | Baltimore Longitudinal Study of Aging (BLSA) | Lys-C | Sep-Pak C18 cartridge | Orbitrap Fusion mass spectrometer (Thermo Scientific) | Electrostatic repulsion-hydrophilic interaction chromatography (20 fractions) | Proteome Discoverer | Swiss-Prot TrEMBL |
Johnson et al. Nat Med, 20206 | BLSA, Mount Sinai School of Medicine Brain Bank, Banner Sun Health Research Institute, Adult Changes in Thought Study | Lys-C and Trypsin | Sep-Pak C18 cartridge | Q Exactive mass spectrometer (Thermo Scientific) | No | MaxQuant | Swiss-Prot TrEMBL |
Mayo Clinic Brain Bank | |||||||
University of Pennsylvania School of Medicine Brain Bank | |||||||
Bai et al. Neuron, 20209 | Brain and Body Donation Program at Banner Sun Health Research Institute | Lys-C and Trypsin | Sep-Pak C18 cartridge | Q Exactive mass spectrometer (Thermo Scientific) | Basic pH HPLC (40–120 fractions) | Jump Suite including SEQUEST and MASCOT | Swiss-Prot TrEMBL UCSC |
Alzheimer’s Disease Research Center at Icahn School of Medicine at Mount Sinai | |||||||
Zhang et al. Acta Neuropathol Commun., 20187 | Emory Center for Neurodegenerative Disease Brain Bank | Trypsin | FASP | LTQ Orbitrap Elite (Thermo Scientific) | No | Proteome Discoverer | TrEMBL (reviewed entries) |
Xu et al. Commun Biol., 201911 | New Zealand Neurological Foundation Human Brain Bank | Trypsin | — | QSTAR Elite Q-TOF spectrometer (AB SCIEX) | Basic pH HPLC (86 fractions) | Protein Pilot | Swiss-Prot |
