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@ARTICLE{Uszkoreit:910685,
      author       = {Uszkoreit, Julian and Barkovits, Katalin and Pacharra,
                      Sandra and Pfeiffer, Kathy and Steinbach, Simone and Marcus,
                      Katrin and Eisenacher, Martin},
      title        = {{D}ataset containing physiological amounts of spike-in
                      proteins into murine {C}2{C}12 background as a ground truth
                      quantitative {LC}-{MS}/{MS} reference},
      journal      = {Data in Brief},
      volume       = {43},
      issn         = {2352-3409},
      address      = {Amsterdam [u.a.]},
      publisher    = {Elsevier},
      reportid     = {FZJ-2022-04057},
      pages        = {108435 -},
      year         = {2022},
      abstract     = {In this article, we present a data dependent acquisition
                      (DDA) dataset which was generated as a reference and ground
                      truth quantitative dataset. While initially used to compare
                      samples measured with DDA and data independent acquisition
                      (DIA) (Barkovits et al., 2020), the presented dataset holds
                      potential value as a benchmark reference for any workflows
                      working on DDA data. The entire dataset consists of 15
                      LC-MS/MS measurements composed of five distinct
                      spike-in-states, each with three replicates. To generate the
                      data set, a C2C12 (immortalized mouse myoblast) cell lysate
                      was used as a complex background for five different states
                      which were simulated by spiking 13 defined proteins at
                      different concentrations. For this purpose, the cell lysate
                      was used in a constant amount of 20 µg for all samples and
                      different amounts of the 13 selected proteins ranging from
                      0.1 to 10 pmol were added, reflecting physiological amounts
                      of proteins. Afterwards, all samples were tryptically
                      digested using the same method. From each sample 200 ng
                      tryptic peptides were measured in triplicates on a Q
                      Exactive HF (Thermo Fisher Scientific). The mass range for
                      MS1 was set to 350–1400 m/z with a resolution of 60,000 at
                      200 m/z. HCD fragmentation of the Top10 abundant precursor
                      ions was performed at $27\%$ NCE. The fragment analysis
                      (MS2) was performed with a resolution of 30,000 at 200 m/z.},
      cin          = {IBG-5},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IBG-5-20220217},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {35845101},
      UT           = {WOS:000828066500003},
      doi          = {10.1016/j.dib.2022.108435},
      url          = {https://juser.fz-juelich.de/record/910685},
}