Proteomics Data and Methods
This page provides information about the data and methods used to generate the Proteomics evidence presented in Agora.
Proteomic evidence for a specific gene can be viewed on the Evidence/Protein tab of that gene’s page in Agora. You can navigate to a gene’s page using search, from the Nominated Targets list, or from the Gene Comparison Tool. You can also compare proteomic evidence across multiple genes using Agora’s Gene Comparison Tool.
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Data and Methods
Protein abundance has been quantified using three different methods; selected reaction monitoring (SRM), tandem mass tagged (TMT) spectrometry, and liquid-free quantification (LFQ):
SRM Data and Methods
SRM data was generated from post-mortem brains of more than 1,000 individuals from the ROSMAP cohort:
Cohort Study | Brain Region |
|---|---|
The Religious Orders Study and Memory and Aging Project (ROSMAP) | Dorsolateral Prefrontal Cortex (DLPFC) |
Samples were analyzed using liquid chromatography (LC)-SRM as described in Proteomics (LC-SRM). The analysis was targeted to proteins found in the consensus AD protein coexpression network described here. Most targeted proteins were measured with a single peptide, resulting in a single measurement per gene rather than protein variant-specific measurements. Some targeted proteins were measured with multiple peptides; for these proteins, the measurement with the smallest p-value is displayed in Agora.
Differential expression of AD versus controls was determined using ANOVA with post-hoc tests. Output consists of log2 fold change for AD cases versus controls (with controls as the reference group), 95% confidence intervals, and FDR-adjusted p-values.
The processed data is available in Synapse through this link: SRM Targeted Proteomics for Agora.
TMT Data and Methods
TMT data was generated from post-mortem brains of 400 individuals from the ROSMAP cohort:
Cohort Study | Brain Region |
|---|---|
The Religious Orders Study and Memory and Aging Project (ROSMAP) | Dorsolateral Prefrontal Cortex (DLPFC) |
Samples were analyzed using isobaric tandem mass tag (TMT) peptide labeling as described in the Round 1 Methods section of Proteomics (TMT quantitation). Batch correction, relative abundance calculation, and log2 transformation was performed as described here.
Differential expression of AD versus controls was determined using linear regression, adjusted for sex and post-mortem interval. Output consists of log2 fold change for AD cases versus controls (with controls as the reference group), 95% confidence intervals, and FDR-adjusted p-values.
The processed data is available in Synapse through this link: TMT Proteomics for Agora.
LFQ Data and Methods
LFQ data was generated from post-mortem brains of more than 500 individuals. Samples were taken from four human cohort studies, representing four different brain regions:
Cohort Study | Brain Region(s) |
|---|---|
Dorsolateral Prefrontal Cortex (DLPFC) | |
Middle Frontal Gyrus (MFG) | |
Temporal Cortex (TCX) | |
Anterior Prefrontal Cortex (AntPFC) |
Samples were analyzed using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Protein abundance was quantified using liquid-free quantification (LFQ). Note that not all proteins are detected in all brain regions; for these proteins, the plots will show fewer than four brain regions.
Samples were harmonized within study by batch correction with COMBAT and regressing out Age, Sex, and Post Mortem Interval (PMI). Differential expression of AD versus controls was determined via ANOVA with an FDR of 0.05.
The processed data is available in Synapse through this link: LFQ Proteomics for Agora.