Subject area	Biology, chemistry
More specific subject area	Phosphoproteomics and mass spectrometry (MS)
Type of data	MS-data, Tab-delimited and Microsoft Excel tables
How data was acquired	Easy-nLC liquid chromatography system coupled to either a LTQ Orbitrap Velos or a TSQ Vantage mass spectrometer (all Thermo Scientific)
Data format	Raw (.raw), mgf peak lists (.mgf), transition lists and Skyline processed files (.csv and.xlsx)
Experimental factors	Sensitivity assessment of different LC–MS approaches using dilution series experiments and application of the most sensitive MS method to quantify MAD1 phosphorylation sites during cell cycle.
Experimental features	Different dilution series of peptides were analyzed using one dimensional liquid chromatography separation and different data-dependent and independent mass spectrometry workflows to assess their limits of quantification. The most sensitive method was applied to monitor phosphorylation site changes in immunopurified MAD1 across different cell cycle stages using thymidine and nocodazole treatment.
Data source location	Basel, Switzerland
Data accessibility	The data are available via ProteomeXchange with identifier PXD000964 http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000964