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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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Neutral losses in MSGF+ #34

Open andrewrobertjones opened 6 years ago

andrewrobertjones commented 6 years ago

Hi, Apologies if I missed it in the docs, is it possible to specify scoring neutral losses on modifications in MSGF+. For some mod types, they will not be identified well (or at all) unless losses of the sidechain can be considered. thanks! Andy

alchemistmatt commented 6 years ago

Good question. Unfortunately, the scoring models cannot be tweaked. If you're concerned that a neutral loss will occur from a dynamic or static post-translational modification, you'd need to update the list of candidate modifications to include the form of the PTM after the neutral loss occurs. Note that PTMs can be specified using either empirical formulas, or via delta mass (positive or negative).

andrewrobertjones commented 6 years ago

Thanks Matt. I was going to search for sulfation which fully loses the side chain mass under HCD, so it's like searching for 79.9 on the precursors but completely unmodified fragments. Do you think this is possible?

sangtaekim commented 6 years ago

Hi Andy, it is difficult but not impossible if you train a new model using ScoringParamGen for such spectra. A tricky part is that to pick up the neutral loss though you'll have to hard code the loss like https://github.com/MSGFPlus/msgfplus/blob/master/src/main/java/edu/ucsd/msjava/msscorer/ScoringParameterGeneratorWithErrors.java#L98.

andrewrobertjones commented 6 years ago

Hi Sangtae. Okay we'll take a look and see if we can adapt it relatively straightforwardly, are there any tricks we should be aware of to build our own copy? best wishes, Andy

sangtaekim commented 6 years ago

I haven't built my copy for too long. Hopefully, @alchemistmatt will be able to advise you.

alchemistmatt commented 6 years ago

We build MSGF+ using IntelliJ IDEA community edition. Clone the msgfplus repo from GitHub, start IDEA, and on the start screen select Import Project then select the pom.xml file. Use the defaults, selecting the Java JDK as the project SDK (we use Java 1.8). To build it, select View, Tool Windows, Maven projects. Expand Lifecycle, right click compile and choose Run Maven Build. If you see "BUILD SUCCESS", it worked. Now right click package and choose Run Maven Build. That build will take longer. Once that succeeds, right click install and choose Run Maven Build. That will create target\MSGFPlus.jar

Training a new model is something that I'm not familiar with, though it is described in the ScoringParamGen reference document.