Database search with multiple sequences

[B@rtenB]

Dear all,

If you obtain sequence data from MALDI-TOFTOF, this means your entries
are all seperate sequences, how do you run a database search with all
those sequences included?

With a Q-TOF search this is no problem since all the peaks-elution
times are one file.

all help welcome,

best regards,

Bart

[Lynette]

Dear Bart,

I'm unsure if I interpreted you question accurately so please correct
me if I'm wrong. If you want to perform a database search results that
contains all your data from the MALDI-TOF-TOF start a new project
using all the data files from your MALDI-TOF-TOF. Select the top most
node which is the project node (contains the path of the project) in
the Project View panel (it should be highlighted now), then select
denovo or Protein ID and set the parameters. The denovo/protein id
results should contain all the results from all the data in your
project.

Best Regards,
Lynette

[B@rtenB]

Thanx for the answer,

If you have seperate MSMS spectra resulting from maldi tof tof, they
are not linked together (in QTOF results, they do!)

the highest node is 'peptide data' ... all the rest are several
fragmentation spectra with a plus '+' sign in front.

I entend to use it for the following:
Identification of proteins from a tryptic in gel digest. So: i cut out
a spot from a 2D-Gel, digest it with trypsin.
The resulting ms spectrum can normally be used for pmf (peptide mass
fingerprinting).
Since There is no genome of the animal i'm working with (do have an
EST) I want to DE NOVO sequence all the fragments resulting from the
digest. All the msms spectra from the fragments, are different
peaklists that I load in to peaks.

So the question is, how do I unite these peaklists and do a database
search with several derived de novo sequences at once!

many thanks,
Bart

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[Lynette]

Dear Bart,

What version of Peaks are you running?

Best Regards,
Lynette

[B@rtenB]

4.5 i think

since the software is in the lab, they have never done an update,
is this possible with other versions?

Bart

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[B@rtenB]

4.5 SP2

[Lynette]

Dear Bart,

It is possible with the Peaks 4.5 SP2 and Peaks 5.1.
In Peaks 4.5 SP2 it's a bit messier. You will have to open all the
files and copy and paste the spectra from the different files into one
file.
In Peaks 5.1 you just have to open the files into the same project and
analyze them as per my instructions above to combine all the results
together into one report.

Best Regards,
Lynette

[B@rtenB]

Dear lynette,

If I well understood your solution I should try the following:

If I have different sequences (peak list files) which peaks manages to
sequence De NOVO, I should somehow try to pool the peaklists in one
textfile?
If I just copy paste, how do I say what the different parent ions
were?
Its not that easy such as just pasting the peaklists together and let
peaks identify for example de novo the three sequences I've pooled?

Best regards,

Bart

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[achim.nepaf]

Hi Bart,

If you contact me by email on info-at-nepaf-dot-com, I can send you an
mgf (Mascot generic format) file, which is a nice example of how you
can concatenate peaklists into one larger file containing many
peaklists. mgf files are compatible with PEAKS and are one way of
importing many spectra. You can either generate them manually (if you
have a limited number of spectra) or you could write a computer
program that does it automatically for you.

Best wishes,
Achim