Facility Computer Room

Proteome Discoverer, Scaffold Q+, Scaffold PTM and other packages are available for use in the facility computer room, LTL 019.  They are free to use and staff are readily available to help.  You may also download the following software onto your own computer.

Scaffold Viewer

Most results sent to customers/users will be in the Scaffold file format.  A fully functional free viewer is available for download from the developer. Proteome Software also has an excellent wikia site.


Princeton LC-MS/MS Data Viewer and Analyzer, a software package for quantitative proteomics including SILAC, 15-N labeling and label-free methodologies.

Proteome Discoverer

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. We strongly recommend that you download PD. PD is free for 30 days, after which PD Viewer can be used to analyze data from our mass spec facility. We also have a copy of PD in the facility computer room, LTL 017, available for your use.

To download PD you will need to register on the Thermo web site. Enter our salesperson's name, Deborah Shanks, in the registration form.


Preview and Byonic are commercial software packages from Protein Metrics which are especially useful for post-translational modification identification.  You may download Preview freely from this site.


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.


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.

Useful Links


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 the videos provided by ASMS.

Thermo Scientific Omics Software Portal

The Thermo Omics 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.

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