There is a newer version of this record available.

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


JSON-LD (schema.org) Export

{
  "description": "<p>The eight&nbsp;raw files serve as a concise but meaningful training data set in the Galaxy training network (https://galaxyproject.github.io/training-material/).</p>\n\n<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 &deg;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&nbsp;of each Spike/in ratio were measured:</p>\n\n<p>Sample&nbsp;&nbsp; &nbsp;HEK&nbsp;&nbsp; &nbsp;E.coli&nbsp;&nbsp; &nbsp;MS method<br>\nSample1&nbsp;&nbsp; &nbsp;2.5&nbsp; &nbsp; &nbsp; 0.15&nbsp; &nbsp; &nbsp; &nbsp; DIA<br>\nSample2&nbsp;&nbsp; &nbsp;2.5&nbsp; &nbsp; &nbsp; 0.15&nbsp; &nbsp; &nbsp; &nbsp; DIA<br>\nSample3&nbsp;&nbsp; &nbsp;2.5&nbsp; &nbsp; &nbsp; 0.15&nbsp; &nbsp; &nbsp; &nbsp; DIA<br>\nSample4&nbsp; &nbsp; 2.5&nbsp; &nbsp; &nbsp; 0.15&nbsp; &nbsp; &nbsp; &nbsp; DIA<br>\nSample5&nbsp;&nbsp; &nbsp;2.5&nbsp; &nbsp; &nbsp; 0.80&nbsp; &nbsp; &nbsp; &nbsp; DIA<br>\nSample6&nbsp; &nbsp; 2.5&nbsp; &nbsp; &nbsp; 0.80&nbsp; &nbsp; &nbsp; &nbsp; DIA<br>\nSample7&nbsp; &nbsp; 2.5&nbsp; &nbsp; &nbsp; 0.80&nbsp; &nbsp; &nbsp; &nbsp; DIA<br>\nSample8&nbsp; &nbsp; 2.5&nbsp; &nbsp; &nbsp; 0.80&nbsp; &nbsp; &nbsp; &nbsp; DIA</p>\n\n<p>Additionally, iRT peptides were added and 1&micro;g of each samples&nbsp;was measured using&nbsp;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&nbsp;24 m/z broad). In the next cycle another&nbsp;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.</p>\n\n<p>Besides the eight raw files, we uploaded a spectral library, a&nbsp;transition list for the iRT peptides as well as an sample annotation file.<br>\nAdditionally, we uploaded&nbsp;the Galaxy PyProphet score&nbsp;training result files: PyProphet score report and PyProphet score.</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Institute for Surgical Pathology, Faculty of Medicine, University of Freiburg", 
      "@type": "Person", 
      "name": "Vogele, Daniel"
    }, 
    {
      "affiliation": "Institute for Surgical Pathology, Faculty of Medicine, University of Freiburg", 
      "@type": "Person", 
      "name": "Stillger, Maren"
    }, 
    {
      "affiliation": "Institute for Surgical Pathology, Faculty of Medicine, University of Freiburg", 
      "@id": "https://orcid.org/0000-0001-7955-2518", 
      "@type": "Person", 
      "name": "Fahrner, Matthias"
    }, 
    {
      "affiliation": "Institute for Surgical Pathology, Faculty of Medicine, University of Freiburg", 
      "@type": "Person", 
      "name": "Schilling, Oliver"
    }
  ], 
  "url": "https://zenodo.org/record/4301690", 
  "datePublished": "2020-11-30", 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/HEK_Ecoli_lib.pqp", 
      "encodingFormat": "pqp", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/iRTassays.tsv", 
      "encodingFormat": "tsv", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/PyProphet_score.osw", 
      "encodingFormat": "osw", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/PyProphet_score_report.pdf", 
      "encodingFormat": "pdf", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/Sample1.raw", 
      "encodingFormat": "raw", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/Sample2.raw", 
      "encodingFormat": "raw", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/Sample3.raw", 
      "encodingFormat": "raw", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/Sample4.raw", 
      "encodingFormat": "raw", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/Sample5.raw", 
      "encodingFormat": "raw", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/Sample6.raw", 
      "encodingFormat": "raw", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/Sample7.raw", 
      "encodingFormat": "raw", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/Sample8.raw", 
      "encodingFormat": "raw", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0b0126be-b3ed-4440-87c2-154e4bd0a2f3/Sample_annotation.txt", 
      "encodingFormat": "txt", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.4301690", 
  "@id": "https://doi.org/10.5281/zenodo.4301690", 
  "@type": "Dataset", 
  "name": "Training dataset: DIA data analysis of a HEK/Ecoli Spike-in dataset using OpenSwathWorkflow"
}
124
503
views
downloads
All versions This version
Views 12448
Downloads 503347
Data volume 472.6 GB354.0 GB
Unique views 9946
Unique downloads 15089

Share

Cite as