search

compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
48 stars 18 forks source link

Peptide shaker file missing. Help Needed!! #167

Closed rlshah closed 8 years ago

rlshah commented 8 years ago

Hello, I have tried running on search GUI first the files from Bruker using the file converter. The output file for peptide shaker doe not open automatically in peptide shaker interface. Can anyone help me in solving this problem. Error message : peptide shaker .cpsx file missing 1

hbarsnes commented 8 years ago

Hi,

Thanks for telling us about this. How did you load the data in PeptideShaker? You have to use the "New Project" option in the PeptideShaker Welcome Dialog when loading data from SearchGUI. Your error seems to indicate that you used the "Open Project" option instead?

Best regards, Harald

rlshah commented 8 years ago

Dear Herald, Thank you very much for the suggestion. I was trying with open project, but now according to your suggestion started with new project option and that worked out.

  1. Can we use this software for label free quantitation or absolute quantitation via AQUA peptide

From: Harald Barsnes [notifications@github.com] Sent: 12 May 2016 12:23:55 To: compomics/peptide-shaker Cc: Shah, Rohan L; Author Subject: Re: [compomics/peptide-shaker] Peptide shaker file missing. Help Needed!! (#167)

Hi,

Thanks for telling us about this. How did you load the data in PeptideShaker? You have to use the "New Project" option in the PeptideShaker Welcome Dialog when loading data from SearchGUI. Your error seems to indicate that you used the "Open Project" option instead?

Best regards, Harald

� You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/compomics/peptide-shaker/issues/167#issuecomment-218718173

rlshah commented 8 years ago

Dear Herald, Thank you very much for the suggestion. I was trying with open project, but now according to your suggestion started with new project option and that worked out.

  1. Can we use this software for label free quantitation or absolute quantitation via AQUA peptide
hbarsnes commented 8 years ago

Hi,

Can we use this software for label free quantitation or absolute quantitation via AQUA peptide

No, I'm afraid not. For label free quantification I'd recommend MaxQuant. I have no experience with absolute quantitation via AQUA so I cannot recommend any software there.

I'm now closing this issue, but please feel free to open a new one if you have other questions.

Best regards, Harald