Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-09-08T16:39:38.067Z
Comments.Text: 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.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-12T12:59:06.857Z
Comments.Text: Could you provide an example dataset? And post the headers and top 5 rows of each file?
Comments.UserDisplayName: Soerendip
Tags: <differential-expression><proteomics><mass-spectrometry>
Title: Mass spectrometry: How to obtain expression counts for protein
ThreadText: # 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
  
  