Program description of “Complementary Finder”
“ComplementaryFinder” is a small jar-program that modifies .mgf files in accordance to
algorithms which were recently published1
Please consider the following notes:
-
High resolution fragmentaion (in this study Orbitrap MS). The number of
complementary pairs relay on the extent of present b and y´ type ions in CAD
spectra. CAD spectra obtain with quadrupole ion traps contain more complementary
b ions than CAD spectra obtained from beam-type instruments.
-
Use Proteome Discover for creating .mgf file and deconvolution/deisotoping.
.mgf format is not a strict format, and all .raw->.mgf convectors produce slightly
different outcome. We cannot guarantee that your convector produces compatible
output and the program will not crash. Decon/Deiso is an extremely important step of
pre-processing files. From our experience, “MS2 spectrum processor” is efficient in
deconvolute CAD MS/MS spectra. Alternatively, you can use Mascot Distiller for
creating decon/deIso mgf files. If you submit ETD data too, we recommend to
perform deconvolution but not deisotoping (due to complicate mechanism of
hydrogen shift it is not possible to distinguish isotopes and forms of c-ions)
-
Sets of consecutive CAD and ETD must have unique scan numbers. If you want
to use CAD and ETD spectra as an input and your data represent more than one run,
you should re-number scans first. RenumberSCANS takes .mgf file of multiple runs
(i.e. SCANS= 1, 2, 3, … 1, 2, 3, …, 1, 2, 3, …) and renumber scans with chosen
factor (i.e.with factor 2000 result will be SCANS= 1, 2, 3, … 20001, 20002, 20003,
…, 40001, 40002, 40003, …)
How to use the software
1. Download the software and place it anywhere on the computer.
2. Double-click on the icon to start “ComplementaryFinder” and you should get a
window as shown on fig 1.
Fig 1. Main page of “ComplementaryFinder”
A. Case I: You have only CAD .mgf files and you performed decon/deIso in PD.
.
1. Press “Open CAD .mgf file…” and choose CAD .mgf file
2. Press “Run” (it becomes active after you have chosen CAD file)
3. Wait for the report (it takes 1 min per 3-5 Mb of .mgf file)
4. Done! The resulting mgf-file will automatically be saved in the same folder as the
original mgf-files.
B. Case II: You have CAD and ETD .mgf files and you performed decon/deIso for
CAD and decon for ETD.
1. Press “Open CAD .mgf file…” and choose CAD .mgf file
2. Press “Open ETD .mgf file…” and choose ETD .mgf file
3. Press “Run” (it becomes active after you have chosen CAD file)
4. Wait for report (it takes 1 min per 3-5 Mb of .mgf file)
5. Done! The resulting mgf-file will automatically be saved in the same folder as the
original mgf-files.
Additionally you can change the default parameters, for example:
C. Case III: You did NOT perform decon/deIso for CAD and/or decon for ETD.
- Mark “Perform decon/deiso” prior to pressing “Run”
D. Case IV: You do not want to make “Intensification”
- Unmark “Perform intensification” prior to pressing “Run”
E. Case V: You don´t want to make “Extraction”
- Unmark “Perform extraction” prior to pressing “Run”
F. Case VI: You want to make “decon/deiso”, but your files were acquired with
another parameters (for instance resolution)
- After choosing files:
- Mark “Perform decon/deiso”
- go to “deco/deiso” tab and change parameters (see Appendix I)
G. Case VII: You want to make “intensification”, but your files were acquired with
another parameters (for instance resolution)
- After choosing files:
- go to “Intensification” tab and change parameters (see Appendix II)
H. Case VIII: You want to make “Extraction”, but your files were acquired with
another parameters (for instance resolution)
- After choosing files:
- go to “Extraction” tab and change parameters (see Appendix III)
Appendix I
Appendix II
Appendix III
1
Kryuchkov F., Verano-Braga T., Hansen T., Sprenger R. and Kjeldsen F. Deconvolution of Mixture Spectra
and Increased Throughput of Peptide Identification by Utilization of Intensified Complementary Ions
Formed in Tandem Mass Spectrometry. J. Proteome Res., Publication Date (Web): June 3, 2013