Yes, it is in there. David
On Mon, Oct 30, 2017 at 5:52 AM, Adam R <[email protected]> wrote: > Hi David, > > Just wanted to ask if the release candidate version that you posted here > in this post (https://groups.google.com/d/msg/spctools-discuss/5NwyzUw3mH > A/ZP8AazR0AwAJ) > contains an updated version of PeptideProphet with an extended mass model > to handle MSFragger processed files? What settings do you recommend > starting with when processing MSFragger output with PeptideProphet? > > Best, > > Adam > > On Tuesday, September 26, 2017 at 11:00:24 AM UTC-5, David Shteynberg > wrote: >> >> Hi Adam, >> >> Yes there is a mode in PTMProphet you can enable called MASSDIFFMODE, it >> will localize the mass difference like a PTM. I have tried this using >> MSFragger and tier-wise open mass searching using SpectraST. >> >> -David >> >> On Mon, Sep 25, 2017 at 11:09 AM, Adam R <[email protected]> wrote: >> >>> Hi David, >>> >>> Thank you for the prompt response! I will give it a try from the command >>> line. I also have a follow-up question to ask to this as I have been >>> wondering about other ways to tackle the data. >>> >>> Gygi's group published a paper in 2015 (http://www.nature.com/nbt/jou >>> rnal/v33/n7/abs/nbt.3267.html) about using wide mass tolerance windows >>> for searching spectra (+/- 500 Da windows) to identify modifications in >>> unassigned spectra. They went on to use the Ascore algorithm to identify >>> the sites of modifcation. I'm wondering whether this would be possible to >>> perform with the current iteration of TPP? (i.e. wide mass tolerant search >>> with comet followed by site analysis by PTM Prophet) PTM Prophet's input >>> requires the amino acid and the mass shifts for PTMs but I'm wondering >>> whether it could be utilized to identify "un-specified" mods on any amino >>> acid. >>> >>> Best, >>> >>> Adam >>> >>> On Monday, September 25, 2017 at 11:47:39 AM UTC-5, David Shteynberg >>> wrote: >>>> >>>> There are a couple things wrong here. Primarily there is a bug in >>>> current distributed version of PTMProphet that prevents it from being run >>>> through the web-interface. There is already a fix available, however, you >>>> will probably want to run this from the command line because of reasons >>>> that follow. Your command needs some adjustment. As is it will try to >>>> localize a different "PTM" on the amino acids you have specified for each >>>> set of amino acids, when what you want it to localize on any amino acid. >>>> You can try the following in a command terminal >>>> >>>> cd c:\TPP\data\[YOUR_DATA_DIRECTORY] >>>> >>>> PTMProphetParser MZTOL=0.2 ABCDEFGHIJKLMNOPQRSTUVXWYZ:639.3169 >>>> [YOUR_INPUT_PEPXML] [YOUR_OUTPUT_PEPXML] >>>> >>>> >>>> Thank you for reporting the issue. >>>> >>>> -David >>>> >>>> >>>> On Sun, Sep 24, 2017 at 11:19 AM, wicher89 <[email protected]> wrote: >>>> >>>>> Hi Everyone, >>>>> >>>>> I am analyzing peptides from cells that have been treated with a UV >>>>> crosslinker attached to a small molecule (ABPP method). This results in >>>>> mono-linked peptides. Because the UV cross-linker is not residue specific, >>>>> I am forced to search the data in comet with a modification of 639.3118 Da >>>>> on any amino acid other than those with fixed modifications. I am able to >>>>> process the output files until the iProphet step, but am running into >>>>> command failure at PTM Prophet. Is there a maximum limit on the number of >>>>> amino acids used at once in a single line entry for a modification? I have >>>>> attached screenshots of the parameters used and the command failure >>>>> output. >>>>> >>>>> Thanks! >>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "spctools-discuss" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to [email protected]. >>>>> To post to this group, send email to [email protected]. >>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at https://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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