Quickstart

The following guide will show how to search example Orbitrap Astral Data with alphaDIA.

1. Prerequisites

Make sure you have installed the GUI using the one-click installer. To verify your installation, open alphaDIA and make sure that the BundledExecutionEngine is selected.

2. Test data

For the first search we will be using a spectral library to search 60SPD bulk HeLa samples on the Orbitrap Astral. Download the test samples and save them: HeLa library, RAW files

3. Search settings

Input Files

Import the library .hdf file and select the thre .raw files. You can select a human .fasta file for reannotation but it’s generally not recommended for empirical spectral libraries.

Method Settings

Although alphaDIA is highly customizable, we will only specify a limited number of settings here. Go to the Search settings and make the following changes:

  • Number of candidates: 5

  • MS1 Tolerance 4ppm

  • MS2 Tolerance 7ppm

Output files

Select an output folder where the search progress and the final results should be saved.

Quickstart using CLI

  1. Clone the repository from GitHub

  2. Create a conda environment called alphadia and install AlphaDIA (either from pip or local, cf. Installation)

  3. cd into the root folder of the repository, then cd test

  4. ./run_e2e_tests.sh basic alphadia will run a basic test after downloading the test data