spctools-discuss

As far as I can tell, you ran the search and tools correctly. But it looks like there are no IDs in

Your search parameters look fine except for using low-res MS/MS settings that you need to change to

Hi, I'm having issues in TPP specifically with decoy proteins appearing in the top results after

Hello everyone, Can you please tell me how can I determine intensity or relative abundance at peptide

Hi david so I get the following message when I click on this script. On Tuesday, December 5, 2023 at

This Scaffold help page lists supported formats including psm.tsv for Fragger: https://support.

Thank you will look into it. Best regards Arpita On Fri, Dec 27, 2024, 02:10 Sebastian Paez <

Hello Can anyone clarify what the 'spscore' and 'sprank' values mean? I want to find

Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.2.0 "Bombogenesis" Just

Thanks alot Jimmy! I read through some of the resources and they are very helpful. Very grateful for

Hello Ash, Thanks for your continued interest in TPP for Mac. Certainly you can change the password

Hi PD users, I wanted to get insight into anyone who has installed PD3 on a computer with AMD Ryzen

Hi everyone, I currently downloaded TPP 7.1 pkg for Mac and I was wondering how to use it as it came

Priti, Can you try these steps below to update Comet from v2024.01 rev. 0 to v2024.01 rev. 1? I'm

Thank you David, everything is clear. I will write to the PEAKS support team tomorrow. Best, Sergio -

Dear all Does anybody know how to use the sofware biotools from bruker and make the analysis of your

Hello, Can you share what version of TPP and on what kind of system it is installed? Did you make any

Hello, Thanks for the help. The problem has been resolved. On Thu, Sep 12, 2024 at 11:24 AM '

Hello everyone, I am learning to use TPP 7.1 by analyzing the example data from the article "TPP

thank you for responding i am using 7.0 version. i haven't tried the lastest one yet, let me try

I agree with this. This is a great new feature in the latest version (7.1.0). In earlier versions we

Hello again Sud! I just ran a test comparing combinations of comet from 6.1 validated with tpp 6.1

Thank you for confirming! On Mon, Aug 5, 2024, 11:37 AM Karla Joanna Rojas Mendez <karla.rojas@ibt

Hello Sud, > 1. I see that in the first image "interact neggamma. pepxml" all the hits

The TPP has tools for extracting searchable fragments from DIA data that can be searched like any

Hi David, Thank you! I see my name in the release note. I'm glad I could help optimize TPP usage.

Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.1.0 "Albedo" We are

Hi Robert, Glad that you got it to install successfully, and thanks for the notes! We'll

Hi Robert, Sorry to hear about the FreeBSD issues. And agree on boost. Thanks again for the kind

Here is the best reference describing iProphet in detail: https://pubmed.ncbi.nlm.nih.gov/21876204/