Output Catalog
ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
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Output Type
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Copica, an open-source easy-to-use protein copy number mass spectrometry database
Advances in mass spectrometry allow profiling proteome with 10 ng material. Copica database aids in analyzing and comparing protein abundance in cells and tissues, highlighting specific proteins and enabling easy comparison of datasets.
CURTAIN, A WEB-BASED TOOL FOR DATA VISUALIZATION AND EXPLORATION OF MASS SPECTROMETRY-BASED PROTEOMICS
Curtain is a tool for sharing, visualizing, and analyzing mass spectrometry data, designed for non-experts. It allows easy data sharing via web links and displays differential analysis results in interactive plots.
CURTAIN-PTM, A WEB-BASED TOOL FOR DATA VISUALIZATION AND EXPLORATION OF MASS SPECTROMETRY-BASED PROTEOMICS (POST TRANSLATIONAL MODIFICATIONS)
Curtain is a tool for sharing, visualizing, and analyzing proteomic and PTM MS data. It allows easy sharing of data via web link, displays results in interactive plots, and enables analysis of protein groups and structure. Free and open-source.
Cactus
Cactus (10.5281/zenodo.7351087) manages session data for curtain and curtainptm backends, handling saving and loading operations efficiently.
Mitochondrial Proteostasis Cryo-ET Analysis
Collection of scripts used for the analysis of cryo-ET data in Ehses et al., 2026. The code, written in MATLAB 2019b, includes pipelines for tomogram pre-processing and reconstruction as well as particle quantification.
Python script used to generate the heatmap representation of identified LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308
Python script used to generate the heatmap representation of identified high-confident LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308.
Python script for Golgi cytoscape analysis
Custom Python script used for the cytoscape network analysis reported in doi.org/10.1101/2022.11.22.517583 (Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content).
Video tutorials for Curtain and Curtain-PTM
Video tutorials to assist users of Curtain and Curtain-PTM proteomic data analysis web tools (described in https://www.biorxiv.org/content/10.1101/2023.07.25.550405v1).
Software for data analysis used in the manuscript “Loss of primary cilia and dopaminergic neuroprotection in pathogenic LRRK2-driven and idiopathic Parkinson’s disease” (doi: 10.1073/pnas.2402206121)
Seurat version 3 was used for single-cell analysis, applying quality control steps to remove outliers and potential multiplets. Scripts and data are available on Dryad (https://doi.org/10.5061/dryad.pk0p2ngvp).
ASAP CRN Cloud Release Notes – Version 4.0.0
ASAP CRN Cloud released version 4.0.0 with expanded datasets including Human Postmortem-derived Brain Sequencing and Mouse datasets. New harmonized collections and individual datasets were added, enhancing research possibilities.
BrainLysoAtlas
Summary: Research by Ghoochani et al. presents a code repository linked to their study on brain lysosomes, identifying SLC45A1-related disease as a lysosomal disorder.
Lysosomal Brain Protein Atlas Interactive Browser
A web tool hosts a proteomic atlas for cell-type-specific queries on LysoIP protein abundance, comparisons, and annotations. Accessible at https://brainresilience.stanford.edu/lysosomal-brain-protein-atlas without login.
