PeptideShaker

Hi Tomasz, > Is there a way to open a file analysed using PeptideShaker 2.2.5 using current

Hi! It would seem like PeptideShaker is not able to read the input files you are giving it. As far as

Hi! Please have a look in the PeptideShaker log file for more details on the issue. You can find the

Hi, I'm afraid that the PRIDE Reshake feature is no longer supported after PRIDE changed their

Hi Harry, You can add custom enzymes in SearchGUI via the Edit > Enzymes menu option at the top of

Hi, Sorry for the late answer! Seems like there was an error in the notification system for the

Hi Wannes, Sorry for the very late answer! Seems like there was an error in the notification system

Hi Volkan, Sorry for the very late answer! Seems like there was an error in the notification system

Hi Mohammed, Sorry for the very late answer! Seems like there was an error in the notification system

Hi Ruben, Splitting up the processing of the samples will make a (most likely) minor impact on the

Thank you for your explanations Harald! Best regards, Ruben On Wednesday, June 16, 2021 at 10:24:49

Hi, Thanks for letting us know. Please see https://github.com/compomics/peptide-shaker/issues/461 for

Hi Zach, I'm afraid it seems like the web service PeptideShaker uses to access the PRIDE data is

Hi all, We've just released a new version of SearchGUI (v4.0.16) that fixes a bug in the

That works perfectly great! Thanks Harald. Best regards, Aik Han On Thu, Jan 21, 2021 at 7:32 PM

Hi again, I forgot to mention that the new releases require Java 9 or newer. So if you're still

To search SWATH files you need to use a different pipeline. You can make your own library and search

Hi, If you have Thermo raw files you can use either ThermoRawFileParser (command line: https://github

Hi, If you have Thermo raw files you can convert them with ThermoRawFileParser, either via the

Hi Vanessa, Here is an updated beta version that should solve the export issues: http://vedlegg.uib.

Thank you! Best regards On Fri, 7 Feb 2020 at 14:58, Harald Barsnes <harald....@gmail.com>

Hi Harald, Here I attach the parameters file I have been using. The PTMs were based on derivatization

Hi Volkan, Having X's in your sequence should not be an issue. Which version of SearchGUI are you

Hi Juan, > I'm guessing you have done a lot of new things with the beta version, but could you

Hi again, Thanks for your answer and the kind words on our work! If you want to normalize to the sum

That's great news! Best. René On Fri., Nov. 22, 2019, 8:23 am Harald Barsnes, <harald.barsnes@

Harald and JC Thank you very much for your reply. I understand the peptide shaker is a much more

Hi Innocent, After SearchGUI, PeptideShaker creates a unified set of peptide-spectrum matches. This

Hi JC, > Is there anything in the validation steps of PeptideShaker that you could see could cause

Hi JC, > I tried before creating a customizable export that contained the intensity of the