Miguel Cosenza-Contreras

Hello Alexey, Many thanks for your answer and your input. It is true that it is not necessary to differentiate between every modification, but some are particularly interesting biologically. In...

Hello @prvst , thanks for your observations. We are using SRA sequencing data from a specific cancer tissue (glioblastoma) to generate a tissue-specific proteogenomic database including SAAVs and indels to...

Hello Felipe @prvst , Many thanks again for taking a look, and for your comments and suggestions. They are really appreciated. I will restructure the headers in a way that...

Hello Felipe @prvst and all, I tested annotating the headers with the simple approach `>Name Description` and now TMT integrator generates empty reports. I avoided using special characters and I...

Hello, After carefully testing several approaches to modify the headers, I noticed that the problem of the small percentage of summarized peptides by TMT integrator wasn't the fault of bad...

Hi @huiyinc , many thanks for taking a look. I will be aware of the `GN=` requirement in the database headers for TMT integrator usage. Best, Miguel

Many thanks for the explanation @huiyinc, for now, it is nice to know how it works so I can include the proper fasta header formatting into my workflow while having...

Hello Chris, Many thanks for your answer and for your guidance, it would definitely make my life easier for navigating through the package structure and to know where to begin....

Hello @svalvaro This looks amazing. Many thanks for sharing. We would definitely give it a try at some point. Best wishes, Miguel

Hello, I am sorry for taking so long to answer. At the time of posting this issue, I was performing several explorative analyses that were kind of abandoned some time...