1. Open Raw File Description Version 2

1.1. Introduction

A standard for storing raw LC/MS experiment data was developed. We term this standard OpenRaw. OpenRaw files were created by the program xr2or, written in Visual C++, using the application programming interface (API) provided by Finnigan. OpenRaw file format has the advantage of being readable on all computer platforms.

Raw data are stored in three functionally distinct folders, contained within a parent folder named after the LC/MS experiment (Supplementary Figure 1a). These folders are: (a) a global parameters folder, (b) an MS spectra archive folder (MS1), and (c) an MS/MS spectra archive folder (MS2).

1.2. The Global Parameters Directory

            The global parameters folder holds four text files. Size.param stores information about the size of the data of an LC/MS experiment, i.e. total number of scans and total number of mass bins. RTSA.param file, which stands for Retention Time Sampling Array, stores information about all the time points at which each mass spectrum was scanned. MSSA.param, which stands for Mass Sampling Array, stores information about the spacing of the sampling points in the m/z dimension given by the mass spectrometer. InstrumentMethod.param stores information about the instrument method used by the user for that particular LC/MS experiment.

1.3. The MS1 Spectra Directory

The MS1 spectra folder contains the file expmnt_name.msar. The extension msar stands for mass spectrum archive and, as the name indicates, it stores the ion-abundance signal from each mass spectrum in concatenated form. A more detailed description of ms2ar can be found in Supplementary Figure 1b.

1.4. The MS2 Spectra Directory

            Similarly, the MS/MS spectra folder stores the file expmnt_name.ms2ar which is a concatenation of the ion-abundance signal for all MS/MS spectra. MS/MS spectra can be analyzed for peptide identification by a separate sequencing program. A more detailed description of ms2ar can be found in Supplementary Figure 1c.