Supplementary Data: Accurate proteome-wide protein quantification from 15N-labeled mass spectra

Data

Raw mass spectra used to generate Figure 2 can be downloaded here: Figure2.zip.

Raw mass spectra used to prepare Figures S2a and S2b can be downloaded here: FigureS1ab.zip.

Raw mass spectra used to generate the table in Additional File 2 can be downloaded here: AdditionalFile2_part1.zip, AdditionalFile2_part2.zip, AdditionalFile2_part3.zip, AdditionalFile2_part4.zip, AdditionalFile2_part5.zip. Extract each of these into the same destination directory.

Tutorials

Analyzing p15N Labeled Data in PVIEW

1. Use Thermo2PVIEW to convert your .RAW files to .mzXML
2. Run PVIEW.
3. Choose "File > Open..."
4. Select the directory containing the .mzXML files
5. Change the quantification mode to "stable isotope pairing (H/L)"
6. Under the "Isotope" tab check the box that says, "Use 15N metabolic labeling."
7. Switch to the MS2 tab and set the precursor tolerance to match your instrument's mass error.
8. Under the "Fixed" tab select any fixed modifications.
9. Under the "Variable" tab select any modifications you've enriched for.
10. Click "Load data..."
11. When processing is complete, select the menu item "Isotope Pairs > Save Tab Delimited."
12. Enter the name of your analysis e.g. "my_analysis.txt"
13. Next launch the R statistical package. Run source("reports.R").
14. Use the function isotope.pair.report("my_analysis.txt") to generate plots that provide an analysis of your data.

For additional information, please visit the Princeton LC-MS/MS Data Viewer and Analyzer (PVIEW) web page.