In UCLouvain-CBIO/msdata2: Data accompanying the Benchmarking package

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Introduction

The msdata2 package mainly contains a set of public accessible quantitative proteomics datasets. The purpose of this package is to provide standard and curated datasets to facilitate the benchmarking work of different identification/quantitative proteomics workflows. Besides aiding benchmarks, msdata2 will also be built as a collection of cleaned, formatted, compressed and extensible proteomics datasets for the research community. We hope msdata2 can also help the other researchers to fulfill their own research interests, as well as other educational or training purposes. Currently, msdata2 mainly consists of analysis results from proteomics workflows. The analysis output has been converted into standard MSnSet object format.

The first dataset in msdata2 is OpenSWATH output from SGS dataset. The The SWATH-MS Gold Standard (SGS) dataset consists of 90 SWATH-MS runs of 422 synthetic stable isotope-labeled standard (SIS) peptides in ten different dilution steps, spiked into three protein backgrounds of varying complexity (water, yeast and human), acquired in three technical replicates. The SGS dataset was manually annotated, resulting in 342 identified and quantified peptides with three or four transitions each. In total, 30,780 chromatograms were inspected and 18,785 were annotated with one true peak group, whereas in 11,995 cases no peak was detected [@Rost2014vh].

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Data Manipulation

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Slide with R Code and Output

summary(cars)

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plot(cars)

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Conclusions

Take a look around the project example for a tour of useful column classes, etc.

References

UCLouvain-CBIO/msdata2 documentation built on July 4, 2020, 10:15 p.m.