raw_data: Example of dataset that contains spike in data for 43...

In Vitek-Lab/MSstatsLOBD: Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

Description

This example dataset is from CPTAC(Clinical Proteomic Tumor Analysis Consortium) assay portan (Thomas and others 2015). The dataset contains spike in data for 43 distinct peptides. For each peptide, 8 distinct concentration spikes for 3 different replicates are measured. The Skyline files for the assay along with details about the experiment can be obtained from this webpage: https://assays.cancer.gov. The particular dataset examined here (called JHU_DChan_HZhang_ZZhang) can be found at https://panoramaweb.org/labkey/project/CPTAC%20Assay%20Portal/JHU_DChan_HZhang_ ZZhang/Serum_QExactive_GlycopeptideEnrichedPRM/begin.view?. It should be downloaded from the MSStats website http://msstats.org/?smd_process_download=1&download_id=548. The data is then exported in a csv file (calibration_data_raw.csv) from Skyline. The csv file contains the measured peak area for each fragment of each light and heavy version of each peptide. Depending on the format of the Skyline file and depending on whether standards were used, the particular outputs obtained in the csv file may vary. In this particular case the following variables are obtained in the output file calibration_data_raw.csv: File Name, Sample Name, Replicate Name, Protein Name, Peptide Sequence, Peptide Modified Sequence, Precursor Charge, Product Charge, Fragment Ion, Average Measured Retention Time, SampleGroup, IS Spike, Concentration, Replicate, light Area, heavy Area. A number of variables are byproducts of the acquisition process and will not be considered for the following, i.e. File Name, Sample Name, Replicate Name, SampleGroup, IS Spike. Variables that are important for the assay characterization are detailed below (others are assumed to be self explanatory):

Usage

raw_data

Format

A data frame with 3870 rows and 16 variables.

Details

• Pepdidesequence Name of the peptide sequence

• Concentration Value of the known spiked concentration in pmol.

• Replicate Number of the technical replicate

• light Area Peak area of the light (measured)

• heavy Area Peak area of the heavy (reference) peptide

Examples

head(raw_data)

Vitek-Lab/MSstatsLOBD documentation built on Dec. 18, 2021, 6:20 p.m.