Dataset Open Access

Training dataset: Generation of a spectral library from HEK-Ecoli Spike-in mass spectrometry data

Vogele, Daniel; Stillger, Maren; Fahrner, Matthias; Schilling, Oliver

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

HEK and E.coli cell pellets were lysed with 5 % SDS, 50 mM triethylammonium bicarbonate (TEAB), pH 7.55. The obtained protein extracts were reduced by adding f.c. 5 mM TCEP and alkylated by the addition of f.c. 10 mM iodacetamide. Protein digestion and purification was performed on S-Trap columns. To ensure protein binding to the S-Trap columns, samples were acidified to a final concentration of 1.2 % phosphoric acid (~ pH 2). Six times the sample volume S-Trap buffer (90% aqueous methanol containing a final concentration of 100 mM TEAB, pH 7.1) was added to the samples which were then loaded on the columns and washed with S-Trap buffer. Protein digestion was performed with trypsin and LysC for one hour at 47 °C. Peptides were eluted in three steps with (1) 50 mM TEAB, (2) 0.2 % aqueous formic acid and (3) 50 % acetonitrile containing 0.2 % formic acid. Eluted peptides of HEK and E.coli were mixed in the following ratios (amount in µg):

Sample    HEK    E.coli    MS method
Sample1    2.5      0.00        DDA
Sample2    2.5      0.05        DDA
Sample3    2.5      0.15        DDA
Sample4    2.5      0.40        DDA
Sample5    2.5      0.80        DDA

Additionally, iRT peptides were added and 1µg of each samples was measured with a Q-Exactive Plus mass spectrometer. Besides the five raw files, we uploaded two fasta files that serve as human and ecoli protein sequence databases, an transition list for the iRT peptides as well as an experimental design for the MaxQuant search.
Additionally, we uploaded the Galaxy MaxQuant training result files: protein groups, peptides, mqpar, msms, evidence and PTXQC.

Files (5.6 GB)
Name Size
Ecoli_database.fasta
md5:eebcf6acbaa69afcc4a2392b1462b670
1.9 MB Download
HEK_Ecoli_exp_design.txt
md5:d0cf64a31dda5269595bd90e5543a82a
159 Bytes Download
Human_database_plus_iRT.fasta
md5:6bb6b6f0e74f4c3109aa7e6855e56f33
13.6 MB Download
iRTassays.tsv
md5:bd8b3dc53e0d1563674ba07172fb05ee
23.1 kB Download
MaxQuant_Evidence.tabular
md5:6a8bd55407833299c35904a96753d3a5
47.7 MB Download
MaxQuant_mqpar.xml
md5:2e3d127bf8c2ced0753ec583dd4913f1
18.8 kB Download
MaxQuant_MSMS.tabular
md5:113c620ed3c168e2b129128ae23d2416
247.2 MB Download
MaxQuant_Peptides.tabular
md5:922af1486e9860d89635a12bc68d8d13
11.8 MB Download
MaxQuant_Protein_Groups.tabular
md5:e63577da85b915a35121b94a9d57aa18
3.4 MB Download
MaxQuant_PTXQC_report.pdf
md5:1a54093b184ccc58db51d656edd26163
320.0 kB Download
Sample1.raw
md5:012718b65f2d26a1be389874fda2a984
1.1 GB Download
Sample2.raw
md5:29b5f59673434b6beb5f5b4ea6ab2a1c
1.1 GB Download
Sample3.raw
md5:322f4e22e25bfa54fd92540d242f3b40
995.1 MB Download
Sample4.raw
md5:9ff022efe81c6a90505b04eb035c98c7
1.0 GB Download
Sample5.raw
md5:fbeecd97635062636faa1a105487f18d
1.1 GB Download
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