Does SAINTexpress-spc actually use the protein length values from the .Prey file?

Samantha_Cassity · January 12, 2026, 9:54pm

I suspected SAINTexpress-spc was not using protein lengths for anything useful. I ran SAINTexpress-spc with a .Prey file that contains UniprotIDs mapped to their correct protein lengths. I also ran it with a .Prey file that contains UniprotIDs mapped to all NAs. Results from both runs are the exact same. This begged the question, what part of the SAINTexpress algorithm is using protein length? Is protein length used at all in SAINTexpress-spc, or is protein length only utilized if I specify optional arguments -L or -R in the command line?

jennaj · January 24, 2026, 12:08am

Welcome @Samantha_Cassity

Hopefully I can help!

The original Galaxy server that hosted this tool (it was the only one) seems to have some unresolved issues and it may not be coming back!

I posted all the ideas I could think of into this topic (when it was last asked). Maybe it also helps you?

SAINTexpress data

Hi @Bernard Hum, this is unfortunate! Because this is an error that only the server administrators can address. This could happen if the server is no longer connected to a computing cluster! Then, this means that you can’t send them a message through the bug reporting system! What to do? Use the original tools/workflows a different way. The Docker version is more likely to be internally stable, however, even this was last touched over 5 years ago! GitHub - bornea/APOSTL: APOSTL is an interactive affinity proteomics analysis software developed to reformat affinity proteomics data (both spectral counting and MS1) for input into the SAINTexpress statistical package and to visualize the output(s). Use currently supported methods instead. The proteomics protocols in the GTN are current and most should work at any of the UseGalaxy servers, with UseGalaxy.eu being the server most are developed against. All → Proteomics / Tutorial List Example → Hands-on: Peptide and Protein ID using SearchGUI and PeptideShaker / Peptide and Protein ID using SearchGUI and PeptideShaker / Proteomics Not the ideal answer, but hopefully adds in some clarification about what happened and your options going forward.