Vogele, Daniel
Stillger, Maren
Fahrner, Matthias
Schilling, Oliver
2020-12-02
<p>The uploaded files serve as a concise but meaningful training data set in the Galaxy training network (https://galaxyproject.github.io/training-material/).</p>
<p>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:</p>
<p>Sample HEK E.coli <br>
Spike_in_1 2.5 0.15<br>
Spike_in_2 2.5 0.80 </p>
<p>Besides the two PyProphet export files, we uploaded a sample annotation file as well as a comparison matrix file.<br>
Additionally, we uploaded the Galaxy MSstats training result files: MSstats_ComparisonResult_export_tabular and MSstats_ComparisonResult_msstats_input.</p>
https://doi.org/10.5281/zenodo.4307758
oai:zenodo.org:4307758
eng
Zenodo
https://zenodo.org/communities/galaxy-training
https://doi.org/10.5281/zenodo.4302083
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
GTN
MSstats
DIA
proteomics
mass spectrometry
Training dataset: Statistical analysis of a HEK/Ecoli Spike-in DIA dataset using MSstats
info:eu-repo/semantics/other