-
Hi Fragpipe developers,
I'm trying to do a protein ID and LFQ of 12 samples using Fragpipe on the CLI, just like many times before. I ran into this issue in the mass calibration and parameter optim…
-
Hello, I want to use DEqMS to analyze my LFQ dataset, which consists of five samples (each in triplicate) and analyze the DEPS among all ten possible comparison pairs. Should I use the values from the…
-
We tried to make paired analyses using the experimental_annotation column "replicate", but this setup
| condition | replicate |
|----------|:-------------:|
| A | 1 |
| A | 2 |
| A | 3 |
| B |…
-
### Description of the Feature
During the benchmark of quantms using LFQ and MBR (issues #300 #301 #287) we developed a new probabilistic algorithm based on SVM that control the number of false posit…
-
Do you have an example (tutorial) how to analyze LFQ phosphoproteomics data?
-
Hi, we have a fractionated LFQ sample and we are wondering what's the best practice for processing this data. We currently do this:
1. MZMLSpectrumReindexer (a custom script that makes the scan ID …
-
Hi there,
I'm trying to run a custom LFQ-offset workflow with Percolator for PSM validation. The problem that FragPipe keep crashing. After the crash workstation got restarted, so I can't save the …
-
Hi there,
I am attaching my code, my inputs and my results after using DEP.
I do not understand how for one condition, the p value (column E of file output "data_results.csv") is bigger than its cor…
-
-
Hi Thang,
Here #7 you have proposed a way to calculate the number of peptides used for quantification to filter the final MaxLFQ table.
I was wondering, how is this different from the option `p…