Hi Luis, thanks for the useful insight, I guess for iTRAQ(8) we need to use
<note>residue modification parameters</note> <note type="input" label="residue, modification mass">46.9955457863@C, 304.205360@[,304.205360@K</note> <note type="input" label="residue, potential modification mass">15.994915@M,304.205360@Y</note> is that correct? thanks a lot, Alberto El martes, 11 de octubre de 2011 20:30:27 UTC+2, Luis escribió: > > Hello Marcus, > As luck would have it, I just had to conduct analysis of an iTRAQ(8) > sample using X!Tandem. > > First, there is unfortunately no GUI to set the parameters for the search, > at least within the TPP. > > Do make sure that you specify the appropriate modifications based on the > chemistry you used to prepare the peptides. Other than alkylation and > MMTS, you should add the isobaric mass tag to all peptides -- typically at > the N-term as well as Lysines, but this might depend on the exact protocol > you followed. Add the following to the "residue, modification mass" tag: > 144.102063@[,144.102063@K . A less abundant potential modification on Y > might be useful to add, under "residue, potential modification mass", > include 144.102063@Y , as well as any other potential mods (e.g. Oxidized > M, etc). > > Also, note that the iTRAQ8-plex reagent has a very different mass > (304.205360), should you ever use that label. > > The standard xtandem/k-score parameters that we ship with the TPP already > exclude fragment ions lower than 125.0 Daltons; you can change this > parameter by adding the following line to your params file, just replace > the value with your desired minimum m/z: > > <note type="input" label="spectrum, minimum fragment mz">125.0</note> > > Hope this helps with your searches, > --Luis > > > > On Mon, Sep 26, 2011 at 11:33 PM, Marcus Sjödin <[email protected] > <javascript:>> wrote: > >> Hi! >> >> I wish to run some iTRAQ labeled data through the TPP using the embedded >> search engine xtandem! The peptides have been alkylated using MMTS and >> labeled with the iTRAQ 4-plex (114-117). The data was acquired on a Waters >> Synapt using DDA mode. I have converted the .raw data to both mzML and >> mxXML format and thus have the data in the format ready to use for the >> database searching. My question regards how to define the search tandem >> parameter file to be set up using isobaric labeling? >> >> Firstly, the default parameter file is set up for carbamidomethylation >> but I need to change it to MMTS which I assume just needs to be changed >> from >> >> <note label="residue, modification mass" type="input">57.021464@C</note> >> >> into >> >> <note label="residue, modification mass" type="input">45.987721@C</note> >> >> >> But how do I define the search for iTRAQ? I assume, a mass addition for >> the isobaric label is needed for the MS scan as well as a exclusion of >> 114-117 in the MS/MS scan is needed? Is there any easy way of doing this? >> Is there a GUI to define the correct search settings for this that works >> with the xtandem in TPP? I would greatly appreciate any help on this topic! >> >> Sincerely, >> Marcus Sjödin >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To view this discussion on the web visit >> https://groups.google.com/d/msg/spctools-discuss/-/d0rlZFFdG6cJ. >> To post to this group, send email to [email protected] >> <javascript:>. >> To unsubscribe from this group, send email to >> [email protected] <javascript:>. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > -- 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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
