This is the dataset for the manuscript "SpectroPipeR - a streamlining post Spectronaut® DIA-MS data analysis R package".

The dataset includes 2 experiments analyzed with Spectronaut® to demonstrate the capabilities of the SpectroPipeR package (results: https://github.com/stemicha/SpectroPipeR_examples).

Example 1:

In the realm of mass spectrometry, species mix experiments have become a standard procedure, routinely employed in facilities worldwide. These experiments are used to benchmark the performance of various methods and devices. For the analysis we used the Exploris480 data from Reder et al., 2023.

The data can be obtained from: https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=0f33717d84fd45b1a318ad40670022cc

Reder, A. et al. MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications. PROTEOMICS (2023) doi:10.1002/pmic.202300294.

Example 2:

In the study from Vitko et al. 2024, plasma samples from 20 late-stage lung cancer patients and 20 control individuals were analyzed using the timsTOF HT mass spectrometer. The samples were processed with the Proteograph Product Suite, which employs five distinct nanoparticles (NP1−5) to compress the dynamic range of the plasma proteome, enabling deeper proteome profiling. Specifically, the NP2 nanoparticle was used for enrichment of plasma. In this example the Evosep/timsTOF HT measurements of NP2 were used.

https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00646

Vitko, D. et al. timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery. J. Proteome Res. (2024) doi:10.1021/acs.jproteome.3c00646.

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Additionally, the dataset includes the R code used for analysis with SpectroPipeR, as well as the source package of SpectroPipeR version 0.4.0 from the accepted manuscript.