Yasset Perez-Riverol

### Description of the bug We need to follow this discussion with msstats and one of our users. https://github.com/Vitek-Lab/MSstats/issues/105 ### Command used and terminal output _No response_ ### Relevant files...

Inmunopeptidomics, quantms and non-enzymatic searches

2

### Description of feature Inmunopeptidomics is one of the use cases that quantms can try to handle in the same way that we are planning to handle Proteogenomics. For Inmunopeptidomics...

proteomicsLFQ fails with empty peptides

5

### Description of the bug Im processing a dataset using proteomicsLFQ and it fails when it found empty list of peptides in one of the idXMLs. ``` TOPPBase.cpp(1605): Value of...

mzTab to verbose with repeated data.

2

### Description of feature @daichengxin @jpfeuffer : I have found that the mzTab files (specially for big projects) are really huge, an mzTab with thousands of mzMLs can end up...

### Description of the bug ``` Error executing process > 'NFCORE_QUANTMS:QUANTMS:SUMMARYPIPELINE (1)' Caused by: Process `NFCORE_QUANTMS:QUANTMS:SUMMARYPIPELINE (1)` terminated with an error exit status (1) Command executed: multiqc \ -f \...

### Description of the bug We have a big error with LFQ data: ``` nf-core/quantms execution completed unsuccessfully! The exit status of the task that caused the workflow execution to...

PXD014414 problems

7

### Description of the bug @daichengxin I have reanalyzed again the dataset PXD014414, if you see the volcano plots almost no proteins are differentially expressed. I was checking the notebooks...

### Description of the bug Project URL: http://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/proteogenomics/benchmakrs/7a81c7b0dd0465b49b39b743bc8d0a/ ### Command used and terminal output _No response_ ### Relevant files _No response_ ### System information _No response_

Error memory TMT dataset PXD012574

5

### Description of the bug URL of the working file: http://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/proteogenomics/benchmakrs/15acadc82868c799e567dd1b219b44/ ``` nf-core/quantms execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was:...

Prepare two full datasets LFQ and TMT for the AWS tests

5

### Description of feature @jpfeuffer and @ypriverol discussed that it would be great to have 2 full datasets, LFQ and TMT for the AWS tests. We need to find from...