Small Introduction about Mass spectroscopy and analyzing the data through a computational tool called MASCOT

1. MASCOT
A Protein Identification Tool
BY
P.S.SHRI VAISHNAVI
1801110012
I M.TECH BIOINFORMATICS
SRMU

2. Introduction
To obtain the information about the protein from
unknown protein sample with respect of its m/z
ratio.
Unknown sample is digested with enzyme,
fragmented peptide is analyzed with existing protein
databases and related protein sequences are aligned
to get to know about the unknown protein.

3. Mass processing operational flow chart[1]

5. Mascot tool
The predominately used tool for mass spectroscopy
is MASCOT by various researchers.
This interactive tool which is helpful for finding the
protein sequences from other related databases.
This is designed from MOWSE (Molecular Weight
Search) which uses the probability for finding the
theoretical spectra by chance.

6. Functional block diagram of web based
interactive searching[2]

7. Protocol for PMF
Obtain the list of sharp peak intensity values from
mass spectrometry data of the unknown sample.
Change the fixed modifications into
carboamidomethyl (H+ and OH- groups should be
added).
Decoy set is invoked to delete the mismatch
sequences during the prediction.
Click submit.

8. MASCOT PMF

9. Results

12. PMF Protein View

14. Mascot sequence Query
This very powerful mode for obtaining the protein
information.
Here all the information related to the proteins say
(amino acid compositions, molecular weight
information and charge involved) are given and it is
very easily we can able to predict the protein.

15. MASCOT Sequence Query

16. Sample notification

21. Conclusion

22. References
1. Josh A. Henkin et al., Mass Processing—An
Improved Technique for Protein Identification with
Mass Spectrometry Data. Journal Of Biomolecular
Techniques, 2004,15, 230-237.
2. David.N.Perkins et al., Probability- based protein
identification by searching sequence databases
using mass spectrometry data. Electrophoresis,
1999,20, 3551-3567.