Tools

Institute of Computing Technology,

Chinese Academy of Sciences,

Beijing, China

Tools for analyzing spectra of core fucosylated glycopeptides: ReapCFuc and DePrecursor.

ReapCFuc: a program for selecting spectra of core fucosylated glycopeptides

DOWNLOAD: ReapCFuc.exe

USAGE: ReapCFuc path c/p

path: the path of the folder where the MS1, MS2, and MS3 files exist.

c/p: set c if the MS3 data are in centroid mode or p if the MS3 data are in profile mode.

STEPS:

Suppose you have a Finnigan RAW file named Raw1.raw, the steps are as follows to get a set of MS3 spectra derived from core fucosylated glycopeptides:

1. Create a folder named Raw1(the same name as the Raw data is recommended) with two blank sub-folders MS2 and MS3.

2. Open Raw1.raw with Bioworks Browser.

3. Extract all MS2 spectra to the MS2 folder. Follow Actions->TurboSEQUEST DTA. Set parameters like below.

4. Extract all MS3 spectra to the MS3 folder. Follow Actions->TurboSEQUEST DTA, changing the pull-down menu MSn to MS3.

5. Extract MS1 spectra to MS1.txt file. Follow Tools->Convert->Spectral Data->Export Text File. (Note: the output file name must be MS1.txt)

6. Install the Matlab Runtime Environment with MCRInstaller.exe(version 2008a, http://www.mathworks.com/). Download ReapCFuc.exe.

7. Execute ReapCFuc in dos command window to process a RAW file. For example,

ReapCFuc D:\Raw1 c

If there are a lot of raw data to process, write a batch file.

8. After taking the above steps, you will find in the folder Raw1 the file Raw1_MS3_Selected.txt and the folder MS3_MHCal which contains the selected MS3 spectra.

If you have any problems, please contact hpwang AT jdl DOT ac DOT cn.

DePrecursor: a program for removing precursor peaks due to glycan fragmentation

DOWNLOAD: DePrecursor.exe

STEPS:

1. Install the MCRInstaller.exe to set Matlab Runtime Environment.

2. Run ‘deprecursor.exe path’ in DOS command window, where path is the directory of spectra.

If you have any problems, please contact yfu AT jdl DOT ac DOT cn.