import peptide sequence?

bechtel...@gmail.com

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Feb 23, 2018, 4:36:13 PM2/23/18

to DeNovoGUI

I have a known molecule and i want DeNovoGUI to use my peptide sequence with my MS data file to determine sequence coverage/modifications of my intact peptide (~4K). I cant find a place to upload my fasta file. When i do a search using only my data there are no common AA sequences to correlate with my known sequence. all of them are random and don't match my molecule

Harald Barsnes

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Feb 26, 2018, 5:52:01 AM2/26/18

to DeNovoGUI

Hi,

To map the de novo results to a FASTA file you can use the Export > Peptide Matches option after loading the results in DeNovoGUI.

If using Novor or DirecTag you can also load the data in PeptideShaker, but then we recommend using SearchGUI to execute the de novo algorithms.

Best regards,

Harald

Charity Bechtel

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Feb 26, 2018, 2:55:53 PM2/26/18

to Harald Barsnes, DeNovoGUI

Do u have a manual on this besides the one online? If I have to wait to run the program before adding the sequence it will still give me the same wrong hits. It’s as though I have to make it smarter before running the program for results

Charity

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Harald Barsnes

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Feb 28, 2018, 7:57:52 AM2/28/18

to DeNovoGUI

Hi Charity,

> Do u have a manual on this besides the one online?

There is no manual besides what is available on the web pages and via the help options inside the tool itself.

> If I have to wait to run the program before adding the sequence it will still give me the same wrong hits. It’s as though I have to make it smarter before running the program for results

I'm afraid that's how de novo searches work. If you know in advance which peptides you are looking for you could consider using target approaches like SRM instead?

Best regards,

Harald

On Monday, February 26, 2018 at 8:55:53 PM UTC+1, Charity Bechtel wrote:

Do u have a manual on this besides the one online? If I have to wait to run the program before adding the sequence it will still give me the same wrong hits. It’s as though I have to make it smarter before running the program for results

Charity

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