Facility Computer Room (LTL 025)
Proteome Discoverer, Scaffold 5, Scaffold Quant, Scaffold PTM, Scaffold Quant and other packages are available for use in the facility computer room, LTL 025, located within LTL 016. They are free to use, and staff are readily available to help. You may also download the following software onto your own computer.
Most results sent to customers/users will be in the Scaffold file format. A fully functional free viewer is available for download.
Scaffold is installed in the facility computer room, LTL 025, and available for your use.
Proteome Discoverer (PD) is commercial software from Thermo Scientific for qualitative and quantitative proteomics. Our mass spec core facility uses PD for all proteomics analyses.
A demo version of PD can be downloaded from Thermo. PD (demo) is free for 60 days, after which PD Viewer can be used to analyze data from our mass spec facility.
PD is installed in the facility computer room, LTL 025, and available for your use.
MaxQuant is non-commercial software for quantitative proteomics. It is designed for large data sets from high-resolution mass spectrometers. It supports both label-free and labeling methods for quantitation.
MaxQuant software can be downloaded from the Max-Planck-Institute of Biochemistry.
MaxQuant is installed in the facility computer room, LTL 025, and available for your use.
Skyline is free software for SRM (selected reaction monitoring), MRM (multiple reaction monitoring), PRM (parallel reaction monitoring for targeted MS/MS), targeted DDA for MS1 (data dependent acquisition), and DIA (data independent acquisition) methods.
Skyline can be downloaded, free of charge, from the MacCoss Lab at the University of Washington.
Skyline is installed in the facility computer room, LTL 025, and available for your use.
The American Society for Mass Spectrometry web site has many mass spectrometry-related resources, including information on the annual ASMS conference, the Asilomar conference, the Sanibel conference, as well as listings of workshops, journals, books, and job postings.
For those interested in an introduction to mass spectrometry, we recommend these videos produced by ASMS.
The Thermo Scientific Software Portal contains various mass spectrometry-related programs which can be downloaded for a 30-day free trial period. The portal also has many informative video tutorials.