Mascot

BYP.S.SHRI VAISHNAVI

1801110012I M.TECH BIOINFORMATICS

SRMU

MASCOTA Protein Identification

Tool

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.

Mass processing operational flow chart[1]

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.

Functional block diagram of web based interactive searching[2]

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.

MASCOT PMF

Results

PMF Protein View

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.

MASCOT Sequence Query

Sample notification

Conclusion

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.