PXD043216
PXD043216 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | DIA analysis from a large scale patient cohort for Cerebrospinal Fluid Biomarker Discovery in Alzheimer Disease |
| Description | Diagnosis of Alzheimer disease (AD) primarily relies on cognitive assessments combined with imaging and cerebrospinal fluid (CSF) biomarkers of amyloid and tau proteins. These biomarkers correlate well with levels of neuropathology, but may be inadequate predictors of cognitive trajectory or treatment response to novel therapeutics. Analysis of larger sets of biomarkers together could improve the diagnosis and prognosis of AD, examine the interaction with and differentiate between comorbid pathophysiologies, and measure treatment efficacy. Here, we report data from a Data-independent Acquisition (DIA) analysis used to simultaneously quantify hundreds of proteins in a large-scale patient cohort from a neurology clinic, all of whom had clinical indication for diagnostic lumbar puncture. We aim to define markers that can stratify and diagnose AD in this clinically-complex cohort. Samples from 408 patients were collected from the clinic according to standardized collection and processing protocols. Samples were prepared in 21 different batches of 24 (23 samples plus one common pool) and analyzed by LC-MS/MS on an Orbitrap Fusion using a DIA method with non-overlapping 25m/z windows from 400-1000 m/z, with a resolution of 120K for MS1 and 60K for MS2. Each sample was injected in duplicate with 4 column washes between each sample. All samples from each batch were run sequentially, with multiples days separating each batch. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-03-26 |
| AnnouncementXML | Submission_2024-03-26_13:45:19.054.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | QC_MGH |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Orbitrap Fusion |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2023-06-22 14:18:49 | ID requested | |
| ⏵ 1 | 2024-03-26 13:45:19 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Alzheimer disease, Biomarker discovery, CSF, Data Independent acquisition, Large scale patient cohort, Batch effect removal |
Contact List
| Steven Arnold | |
|---|---|
| contact affiliation | Massachusetts General Hospital |
| contact email | searnold@mgh.harvard.edu |
| lab head | |
| Becky Carlyle | |
| contact affiliation | Massachusetts General Hospital and Harvard Medical School |
| contact email | bcarlyle@mgh.harvard.edu |
| lab head | |
| QC_MGH | |
| contact affiliation | CHU Qc U.Laval / MGH |
| contact email | florence.roux-dalvai@crchuq.ulaval.ca |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/v05/MSV000092241/ |
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