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Introduction
MSIght is an open-source Python-based algorithm designed for proteome characterization from the automated integration of histology, LC-MS/MS, and MSI datasets.
MSIght is freely available for download from GitHub (https://github.com/lingjunli-research/MSIght).
MSIght is only supported for use with Windows OS, though limited functionality may be available with MacOS and Linux/UNIX. MSIght is capable of running on a standard personal computer. For our purposes, the program was validated on a Windows Desktop computer with the following specifications: Processor: Intel(R) Xeon(R) CPU E5-1607 v3 @ 3.10GHz Installed RAM: 128 GB System Type: 64-bit OS System: Windows 10
We recommend using Anaconda (https://www.anaconda.com/download) to run MSIght, and most requirement packages will be present in the initial Anaconda download. The program also requires access to MSFragger via FragPipe. This can be downloaded free of charge here: https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html
For LC-MS/MS files, MSFragger can handle both .RAW or .MZML files. For imaging data, MSIght requires .imzML file format. This data can be uploaded in either centroid or profile mode, with centroid being more efficient.