Dataset Open Access

Training dataset: Statistical analysis of a HEK/Ecoli Spike-in DIA dataset using MSstats

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

The uploaded 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 two different ratios and four replicates of each Spike/in ratio were measured and analysed using OpenSwathWorkflow in Galaxy. Results were exported using PyProphet and can be used for the statistical analysis and detection of the two different Spike-in Ratios. The Spike-in ratios were the following:

Sample        HEK    E.coli   
Spike_in_1    2.5      0.15
Spike_in_2    2.5      0.80 

Besides the two PyProphet export files, we uploaded a sample annotation file as well as a comparison matrix file.
Additionally, we uploaded the Galaxy MSstats training result files: MSstats_ComparisonResult_export_tabular and MSstats_ComparisonResult_msstats_input.

Files (377.2 MB)
Name Size
Comp_matrix_HEK_Ecoli.txt
md5:c5ddc65a019d3b914f48847b625d5cc2
55 Bytes Download
MSstats_ComparisonResult_export_tabular.tsv
md5:d55269045e54a8683f6895b25894c816
705.6 kB Download
MSstats_ComparisonResult_msstats_input.tsv
md5:c5843df59184c183cf9f04fad617bbba
611.3 kB Download
PyProphet_export.tabular
md5:5be938cc98998c4b2db279ee3b6a274d
300.7 MB Download
PyProphet_msstats_input.tabular
md5:36c60433a79ca77e613d7f04d123631f
75.2 MB Download
Sample_annot_MSstats.txt
md5:6378ab8185222bbb00a62954945da563
460 Bytes Download
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