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Hi,
we are performing open searches on QE data from mouse and I feel that something is missing in FragPipe: if I label several experiments, then I get a nice peptide.tsv in each experiments' direct…
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```
(Collect change requests for the CV here.)
[Term]
id: PI:00216
name: sequest:PeptideRank
def: "The SEQUEST result 'Rank' in out file (peptide)." [ref:ref]
is_a: PI:00153 ! search engine specific …
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Hi there, is there a way to merge the psm.tsv files post-analysis? There doesn't seem to be a common denominator I could use to merge it myself, or am I missing sth? Thanks for your help
Raphael
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Hi
I am analyzing quite a lot of DIA data using DIA-NN. For the most runs I have processed, it takes about 40-60 mins but there are few runs that took longer around 200 mins. The .dia file sizes are…
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Are these the same?
GO:0016971
flavin-linked sulfhydryl oxidase activity
Catalysis of the formation of disulfide bridges.
GO:0015035 | protein disulfide oxidoreductase activity
Catalysis of…
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Dear Developers,
Finally I run my fragpipe-workflow (LFQ-MBR) completely from a script (that was developed with a smaller DB and it run successfully).
Using now my large MetaproteomicsDB I end u…
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Hello MSFragger team,
I try to use MSFragger (through FragPipe) to search phosphorylation data from Bruker’s TimsTOF pro. However, all intensity values for proteins and peptides are 0 in the search…
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Hello,
I've been trying to apply the Philosopher pipeline to a recently published [CPTAC proteomics dataset](https://www.sciencedirect.com/science/article/pii/S0092867420314513). The workflow appear…
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I observe the following error when running SearchGUI from Galaxy (using the latest version available for Galaxy, i.e. 4.0.12)
```
Fri Mar 12 15:12:56 CET 2021 Importing spectrum files.
10% 20% 30…
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Galaxy server : usegalaxy.eu
History link: https://usegalaxy.eu/u/_luisfr/h/peptidegenomiccoordinateissue
Tool version : Galaxy Version 0.1.1
While executing **Peptide Genomic Coordinate (followi…