Non-standard amino acids

[iainiai]

Someone just asked me a good question about how to use PEAKS when we
have to consider non-standard amino acids. The answer is to 'trick'
PEAKS by defining a PTM. If we apply a variable modification to, say,
methionine, PEAKS will have to consider both the M and the modified M.
Essentially, this increases the software's vocabulary.

So in the case of a non standard amino acid with mass 'x' we choose an
arbitrary amino acid, C, and define a modification with mass = x -
mass(C) ... then apply it as a variable modification on C.

If you don't know the mass x, but have a chemical formula, I found a
calculator that you can use: http://www.ch.ic.ac.uk/java/applets/f2m2f/
Don't forget that the formula should correspond to the amino acid *in
sequence*, i.e. the residue.

Best,
-IainR

[Peter M Yau]

Hi Iain,

I have noticed that Peaks Online takes in a submitted file (say for
example , Q_ToF_07-064 sample 3) and after analysis with Peaks
Online, returned the results with absolutely no reference to the data
file. I run many many samples at a time. This system is insane
!! How do you suppose that we track our results ? Help !!

Peter

[iainiai]

Hi Peter,
Two things to discuss here:
1) If you submit a search via the web interface, the results file
returned should be named after your data file plus some digits
representing a job number (because you may submit the same file more
than once). An example would be Q_ToF_07-064
sample38427669948997133593.pkl.anz.

2) If you submit a search via PEAKS Client (or using PEAKS Studio as a
Client) the results will be returned directly to PEAKS Client (or
PEAKS Studio) as long as you leave PEAKS Client/Studio open. So you
don't have to worry about what the server calls it. When you save a
file in PEAKS Studio or PEAKS Client, the default is to save it as the
same name as the original data file, but with the .anz. When the
results are returned to the PEAKS Client/Studio, you will also get an
email notice, in which it will call the results file something
seemingly random. But the name of the original data file is always
noted in that same email.

In the next release of PEAKS Online, we'll have more comprehensive
user management. Part of this means that each user will be able to see
all his/her search history, and all searches that he/she has been
granted permission to view. It will list the name of the original file
here as well.

I hope that addresses your concern. Thanks for posting :-D

Best,
-IainR