Does Data-Independent Acquisition Data Contain Hidden Gems? A Case Study Related to Alzheimer’s Disease

Abstract

One of the potential benefits of using data-independent acquisition (DIA) proteomics protocols is that information not originally targeted by the study may be present and discovered by subsequent analysis. Herein, we reanalyzed DIA data originally recorded for global proteomic analysis to look for isomerized peptides, which occur as a result of spontaneous chemical modifications to long-lived proteins. Examination of a large set of human brain samples revealed a striking relationship between Alzheimer's disease (AD) status and isomerization of aspartic acid in a peptide from tau. Relative to controls, a surprising increase in isomer abundance was found in both autosomal dominant and sporadic AD samples. To explore potential mechanisms that might account for these observations, quantitative analysis of proteins related to isomerization repair and autophagy was performed. Differences consistent with reduced autophagic flux in AD-related samples relative to controls were found for numerous proteins, including most notably p62, a recognized indicator of autophagic inhibition. These results suggest, but do not conclusively demonstrate, that lower autophagic flux may be strongly associated with loss of function in AD brains. This study illustrates that DIA data may contain unforeseen results of interest and may be particularly useful for pilot studies investigating new research directions. In this case, a promising target for future investigations into the therapy and prevention of AD has been identified.

The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data

“…The files contain the suggested peptide or peptides matched to each spectrum, but these matches must then be vali-Figure 5: DIAmeter analysis of three Alzheimer's samples. Three samples from a recent Alzheimer's study [22] were searched against the Uniprot human reference proteome. The figure shows the number of peptides that were detected at a 1% FDR threshold in all three runs, in any combination of two runs, and in single runs.…”

“…Here, we demonstrate how to run the software and show that it gives consistent results on several DIA runs from a recently published study. In this analysis, we use data from a large-scale Alzheimer's study [22], selecting three runs at random from the hippocampus brain region, batch 1. To search a file "HZR03.mzml" against the Uniprot human proteome ("human.fa") requires two steps:…”

Distinguishing post‐translational modifications in dominantly inherited frontotemporal dementias: FTLD‐TDP Type A (GRN) vs Type B (C9orf72)

“…PTMs may regulate protein conformation, biophysical properties, protein interactions, function and subcellular localisation [14,15]. Although PTMs occur physiologically, many have been detected in association with protein aggregates in diverse neurodegenerative diseases [14,[16][17][18][19][20][21].…”

Proteomics of resilience to Alzheimer’s disease identifies brain regional soluble Aβ levels, actin filament processes, and response to injury

“…Here, we have used data independent acquisition (DIA) MS/MS proteomics of soluble protein extracts from multiple brain regions donated by comprehensively evaluated research participants who were normal controls (NC) free of clinically significant brain diseases, had actual RAD, or had AD dementia (ADD) without significant comorbidities [9]. Our differential expression analysis performed for each brain region identified 33 RAD-associated differentially expressed proteins (DEPs).…”