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Published April 29, 2020 | Version v1
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Training dataset: Mass spectrometry based proteomics of healthy human serum samples

  • 1. Institute for Surgical Pathology, Medical Center – University of Freiburg, Germany
  • 2. Institute of Molecular Medicine and Cell Research, Medical Center – University of Freiburg, Germany


The two raw files serve as a concise but meaningful training data set in the Galaxy training network (

Serum of a healthy person was obtained by centrifugation of full blood in a serum-gelmonovette. One serum sample was depleted for high abundant proteins, the other not.
For the non-depleted sample: 5µl of serum was diluted with 0.1% Rapigest, resulting in a concentration of 1mg/ml.
Depletion was performed with the Seppro IgY14 Spin columns which are able to deplete 14 high abundent blood proteins by immunoaffinity. For the depleted sample 9µl of serum was diluted with TBS/HCl/NaCl buffer and added to the Seppro IgY14 spin column. After depletion the sample was buffered with Hepes pH 8.0 and Rapigest was added to a final 0.1% Rapigest concentration. From here on, both samples were reduced by adding TCEP, alkylated by IAA and quenched with DTT in solution. Digestion was performed by adding trypsin in a ratio of 1:50 to the samples. After incubation at 37°C, 600rpm, over night, the sample clean-up was performed with the PreOmics desalting columns. iRT peptides were added and the sample was measured with a Q-Exactive Plus mass spectrometer. Besides the two raw files, we uploaded a fasta file that serves as human protein sequence database and the Galaxy MaxQuant training result files: protein groups, peptides, mqpar and PTXQC.



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