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Dataset Open Access

Training dataset: Mass spectrometry based proteomics of healthy human serum samples

Steenbuck, Derya; Mayer, Bettina; Schilling, Oliver; Föll, Melanie

The two raw files serve as a concise but meaningful training data set in the Galaxy training network (https://galaxyproject.github.io/training-material/).

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.

Files (1.1 GB)
Name Size
MaxQuant_mqpar.xml
md5:2268b82319fac7aafe8747deed68078c
17.7 kB Download
MaxQuant_Peptides.tabular
md5:e2654cb40dbdcb3b802530b9c88f0c06
836.8 kB Download
MaxQuant_Protein_Groups.tabular
md5:cdf1f16a33b80fa6f19d2ef1c00a91c2
170.2 kB Download
Protein_database.fasta
md5:ef65ff8e4bbfc17d3d2b75d514175bed
13.6 MB Download
PTXQC_report.pdf
md5:19e44325f1298e493183d56742f3b748
56.1 kB Download
Sample1.raw
md5:34402bf7a61eaae9f5b31a5e09e21fd9
497.5 MB Download
Sample2.raw
md5:110b903dc800204a9d423a41b057ba25
613.6 MB Download
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