PeptideShaker

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

Thanks a lot Innrt for your detailed answer. Very Helpful! Best, Bassel On Monday, March 25, 2019 at

Dear Dmitry, Thanks for the kind words. CoIP are tricky, I often see the bait alone or half of

Dear Sameh. I faced a similar problem, performing quantification on label-free DDA data, a few months

Thanks Sent from my Sony Xperia™ smartphone ---- Harald Barsnes wrote ---- Hi Stoyan, You can find

Hi Valentine, I don't see anything obviously wrong with your search parameters. And unless your