spctools-discuss

Dear friends, I am trying to kill a job which was taking too much time. I even uninstalled the

Hello James, Yes, these values are still hard-coded. If you wish to test alternative values, you can

Hi Sudarshan, I don't use the TPP much. It looks like InteractParser is trying to read a file it

You would put 1 in that box, since you know you injected 1 ug. On Thursday, December 17, 2020 at 7:14

Hi Sud, I think you can do that with excel. Select the cells that have the modified peptides. Use the

Thank you David, I tried with another file. It worked. But can you please tell me about the

Thank you. I will try that. Em ter., 15 de dez. de 2020 às 01:52, sudarshan kumar <kumarsudershan@

Thank you so much Eric, I will use this.... Regards On Fri, Dec 11, 2020, 05:06 'Eric Deutsch

Hi, I have two treatment groups and want to identify (& quantify) the peptides. 1. Metabolic

Dear David, Thanks for explaining the principle of multiple match. I was asking if there is any flag

Hello Mehar, I am looking at the message that says you have 0 PSM in the input to the iProphet. This

The script works perfectly without any error! Thanks for your help. On Thu, Dec 3, 2020 at 6:43 AM

Hi， Thanks for your answer. -I can see that "tandem.exe" processes is running by opening

Hello Soroush, Great! Good to verify that it is working as designed. And you will not miss those zero

Hi, Comet does have a parameter for generating an internal decoy database: http://comet-ms.

Hi Miguel, Glad that you were able to solve this, and sorry we could not help, as we do not have

Not a problem! In the end I decided just to remove all of the titins from my database - it shouldn

Hi Nathan, In case you want to build something that closely resembles 5.2.0, you can follow the steps

Thanks! On Thu, 22 Oct 2020 at 17:11, Mark Athanason <mark.athanason@gmail.com> wrote: If you

Hi I want to run TPP on a Linux server of our institute. However, I'm not a super user so I

Hi Eric, Thank you for the answer. I will try whether I could build such a fasta from the log file.

You can get a recipe for using TPP with Docker here: http://tools.proteomecenter.org/wiki/index.php?

Hi, eg I used X!Tandem in the past when searching for point mutations in proteins. For most tasks, I

For LFQ and sample comparison, you also could try ProtyQuant, which uses TPP pepXML (PeptideProphet

Both worked! Thanks so much! On Thursday, October 1, 2020 at 10:55:24 AM UTC-5 jwi...@gmail.com wrote

Hello Aziz, X!Tandem parameters are in XML format. You can learn about them at their website: https:/

This looks great! Thank you. Robert! --Luis On Fri, Sep 25, 2020 at 1:34 PM Robert <robert.winkler

Thanks! I do have less error tables than I would expect. When I ran PeptideProphet, I received the

Hi, I have generated spectral libraries following the Nature Protocols paper in 2015. There are

Carbamidomethylation has a modification mass of 57.021464. To apply it to each peptide's n-