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Dataset Open Access

Training dataset: DIA data analysis of a HEK/Ecoli Spike-in dataset using OpenSwathWorkflow

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

The six 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 two different ratios and triplikates of each Spike/in ratio were measured:

Sample    HEK    E.coli    MS method
Sample1    2.5      0.05        DIA
Sample2    2.5      0.05        DIA
Sample3    2.5      0.05        DIA
Sample4    2.5      0.15        DIA
Sample5    2.5      0.15        DIA
Sample6    2.5      0.15        DIA

Additionally, iRT peptides were added and 1µg of each samples was measured using data independent acquisition with a Q-Exactive Plus mass spectrometer. Briefly, a scan range from 400-1000 m/Z was first covered by an MS1 scan followed by 25 consecutive MS2 scans (each 24 m/z broad). In the next cycle another MS1 scan was acquired followd by 26 MS2 scans (also 24m/z broad) in which the window centers were shifted by 50% compared to the previous cycle of MS2 scans. The resulting raw files contain overlapping MS2 scans.

Besides the six raw files, we uploaded a spectral library, a transition list for the iRT peptides as well as an sample annotation file.
Additionally, we uploaded the Galaxy PyProphet score training result files: PyProphet score report and PyProphet score.

Files (13.4 GB)
Name Size
HEK_Ecoli_lib.pqp
md5:679d0ee98149e0ef0ff6912ca4efe3bb
170.4 MB Download
iRTassays.tsv
md5:bd8b3dc53e0d1563674ba07172fb05ee
23.1 kB Download
PyProphet_score.osw
md5:ee759ced475d20b91fababe35fbd2f37
4.6 GB Download
PyProphet_score_report.pdf
md5:e7d0e46178d023189ad6af0c29e96abe
27.3 kB Download
Sample1.raw
md5:14586fe6ee523ba45935d75b4a5f0620
1.4 GB Download
Sample2.raw
md5:903ffa00de151d8c7dee9735fbac52c5
1.5 GB Download
Sample3.raw
md5:9a24538278b00bb2d3ccfc1ad7209fd6
1.4 GB Download
Sample4.raw
md5:af5ce92212f8b7a7c553d5b4f4f5cb62
1.5 GB Download
Sample5.raw
md5:991b81e9b10d2d694bc6f6effdf8eb01
1.4 GB Download
Sample6.raw
md5:7915c05923748742b2b8c17f7782209b
1.4 GB Download
Sample_annotation.txt
md5:861bd8c072f7f79def97c61e85a30c5b
228 Bytes Download
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