<p>I was given a data set consisting of 6 samples: 3 control and 3 treated. I dont have information about how data were generated and what the outputs represent.</p>
<p>Each sample corresponds to a folder within which there are the following files:</p>
<p>&quot;DB search psm.csv&quot; &quot;de novo only peptides.csv&quot; &quot;de novo only peptides.xml&quot; &quot;de novo only spectra.mgf&quot; &quot;filter.csv&quot; &quot;peptide features.csv&quot;
&quot;peptide.csv&quot; &quot;peptides_1_1_0.mzid&quot; &quot;peptides.pep.xml&quot; &quot;protein-peptides.csv&quot; &quot;proteins.csv&quot; &quot;proteins.fasta&quot; &quot;PSM ions.csv&quot;</p>
<p>The &quot;peptide.csv&quot; files have the following column names:</p>
<p>Peptide -10lgP Mass Length ppm m/z RT 1/k0 Range Area Ctrl-2 Fraction Precursor Id Source</p>
<p>The &quot;proteins.csv&quot; files have the following column names:</p>
<p>Protein Group Protein ID Accession -10lgP Coverage (%) Coverage (%) Ctrl-1 Area Ctrl-1 #Peptides #Unique #Spec Ctrl-1 PTM Avg. Mass Description</p>
<p>Has anybody ever worked with these type of data?</p>
<p>I would like to do exploit these data and perform a differential analysis but i don't know how to create a SummarizedExperiment from these data.</p>
<p>Any help would be greatly appreciated.</p>
<p>Thank you</p>

CC BY-SA 4.0
2022-09-08T16:39:38.067Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2023-01-12T12:59:06.857Z
Could you provide an example dataset? And post the headers and top 5 rows of each file?
Soerendip
<differential-expression><proteomics><mass-spectrometry>
Mass spectrometry: How to obtain expression counts for protein
# Mass spectrometry: How to obtain expression counts for protein

(Asked by: username_0 on 2022-09-08)

I was given a data set consisting of 6 samples: 3 control and 3 treated. I dont have information about how data were generated and what the outputs represent.

Each sample corresponds to a folder within which there are the following files:

"DB search psm.csv" "de novo only peptides.csv" "de novo only peptides.xml" "de novo only spectra.mgf" "filter.csv" "peptide features.csv"
"peptide.csv" "peptides\_1\_1\_0.mzid" "peptides.pep.xml" "protein-peptides.csv" "proteins.csv" "proteins.fasta" "PSM ions.csv"

The "peptide.csv" files have the following column names:

Peptide -10lgP Mass Length ppm m/z RT 1/k0 Range Area Ctrl-2 Fraction Precursor Id Source

The "proteins.csv" files have the following column names:

Protein Group Protein ID Accession -10lgP Coverage (%) Coverage (%) Ctrl-1 Area Ctrl-1 #Peptides #Unique #Spec Ctrl-1 PTM Avg. Mass Description

Has anybody ever worked with these type of data?

I would like to do exploit these data and perform a differential analysis but i don't know how to create a SummarizedExperiment from these data.

Any help would be greatly appreciated.

Thank you

**Tags:** differential-expression, proteomics, mass-spectrometry
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: Could you provide an example dataset? And post the headers and top 5 rows of each file?  

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## 0 answers

