-
Hello Fragpipe team,
I am trying to analyze results from a mass-offset search. In the psm.tsv output, there are some PSMs with a reported 'Modified Peptide' but no 'Assigned Modification'. These on…
-
Hello DiaNN team,
I have been using DiaNN to analyze histone modifications. The peptides we are analyzing are first derivatized using propionic anhydride, so many of the modifications are combinati…
-
Hiya!
Thanks for such a wonderful package. I'm working with a lot of peptides that I order from GenScript. A lot of these have modifications or are non-natural amino acids (see [here](https://www.g…
-
Hi,
I want to analyze LFQ-DIA global proteome and phospho-enriched proteome data separately on DIA-NN. Just want to make sure that we need two different libraries for these two different searches, r…
-
Hi,
I am interested in modifying FragFold to support custom tiling offsets for fragment generation. For example, a 3 aa increment when generating fragments could speed up peptide binding prediction…
-
Hello Fengchao and others on the IonQuant team,
Using Fragpipe, I am searching for modified peptides with the labile/detailed mass-offset search and quantifying with IonQuant. I have one fixed modi…
-
I have the same issue with this #1310 unable to resolve. The error happens when searching specific PTM modifications search, like below. I used TMT11 plex. The monoisotopic mass of 156.1151 on CHK and…
-
I really like pepquery and have found this to be a valuable tool. However, I would also love to be able to search for specific modifications using the web version. Is there a way to input a peptide to…
-
Hello
I am trying to run the pepquery web application and got this error
Error message: simpleWarning in system(javabin, intern = TRUE): running command 'java -Xmx50G -jar tool/pepquery.jar -c…
-
Hello Vadim and Team,
I am using a spectral library for modified histone peptides that I built in skyline. I have some questions regarding using this library...
1. What is the best way to conver…