ptmprophet flags

[PePito-M]

Hi,

I am using Philosopher(build=1626989421, version=v4.0.0) and have a specific interest in PtmProphet (v4.0.0).
Thank you for making these tools available, they are quite something.

I have notice that the flags stated in wiki are different from the ones accepted in this version.
Please see below the flags currently accepted:

I have been trying to find more information on what the different flags do and what can their impact in the phosphosite probabilities be.
Is there some documentation that I have missed? Could you please point to where this kind of explanation can be found, if exist, or explain a little better what some these flags do?

I have a particular interest in these flags:
--autodirect
--direct
--ifrags
--massdiffmode
--lability

Thanks,
Pedro

[sarah-haynes]

Hi Pedro, thanks for pointing out the missing flags in the wiki. There is a bit more information about them in a supporting file from the PTMProphet publication: (https://github.com/Nesvilab/philosopher/files/7332837/pr9b00205_si_002.pdf)

AUTODIRECT Use direct evidence when the lability is high, use in combination with LABILITY
DIRECT Use only direct evidence for evaluating PTM site probabilities
IFRAGS Use internal fragments for localization (default: do not use internal fragments)
MASSDIFFMODE Treat the mass difference between measured and theoretical mass as a modification and localize
LABILITY Compute Lability of PTMs

You can also see the publication itself for more information. Was there a specific question you had?

Sarah

[PePito-M]

Hi Sarah,

thanks for the reply.
I have read trough both documents but I still have some specific questions about the --direct and --ifrags flags.

Just for simplification purposes, imagine we have this peptide sequence :
RRSLT
I want to check for phosphorylation events. It can be on the Serine, position 3, or Tyrosine, position 5.
1- If I use the --direct flag, does that mean that ptmprophet will only take into account b3-ion and y3-ion when calculating the probability of the phosphorylation being in position 3? Would that be what direct evidence means?
2- If I want ptmprophet to take into account a possible b4-ion, that might show that a phosphorylation occurred in the first 4 residues, would I need to use the --ifrags flag?

Thank you in advance,
Pedro

[sarah-haynes]

--ifrags likely refers to true internal fragment ions (i.e., not b or y ions), but we're not sure exactly what --direct does, you may want to ask the PTMProphet developers on the SPC tools google group