Lect13 Quantitation and other applications

An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)

Info iconThis preview shows pages 1–11. Sign up to view the full content.

View Full Document Right Arrow Icon
Fa 06 CSE182 CSE182-L13 Mass Spectrometry Quantitation and other applications
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Fa 06 CSE182 What happens to the spectrum upon modification? Consider the peptide MSTYER. Either S,T, or Y (one or more) can be  phosphorylated Upon phosphorylation, the b-, and y- ions shift in a characteristic fashion.  Can you determine where the  modification has occurred? 1 1 6 5 4 3 2 5 4 3 2 If T is phosphorylated, b 3 , b 4 , b 5 , b 6 , and y 4 , y 5 , y 6 will shift
Background image of page 2
Fa 06 CSE182 Effect of PT modifications on identification The shifts do not affect de novo interpretation too much. Why? Database matching algorithms are affected, and must be changed. Given a candidate peptide, and a spectrum, can you identify the  sites of modifications
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Fa 06 CSE182 Db matching in the presence of modifications Consider MSTYER The number of modifications can be obtained by the difference in parent mass. With 1 phosphorylation event, we have 3 possibilities: MS*TYER MST*YER MSTY*ER Which of these is the best match to the spectrum? If 2 phosphorylations occurred, we would have 6 possibilities. Can you compute more  efficiently?
Background image of page 4
Fa 06 CSE182 Scoring spectra in the presence of modification Can we predict the sites of the modification? A simple trick can let us predict the modification sites? Consider the peptide ASTYER. The peptide may have 0,1, or 2 phosphorylation events. The difference of the parent mass  will give us the number of phosphorylation events. Assume it is 1. Create a table with the number of b,y ions matched at each breakage point assuming 0, or 1 modifications Arrows determine the possible paths. Note that there are only 2 downward arrows. The max scoring path determines the  phosphorylated residue A S T Y E R 0 1
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Fa 06 CSE182 Modifications Modifications significantly increase the time of search. The algorithm speeds it up somewhat, but is still expensive
Background image of page 6
Fa 06 CSE182 Fast identification of modified peptides
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Fa 06 CSE182 Filtering Peptides to speed up search Filter Significance Score extension De novo Db 55M peptides Candidate Peptides Database MDERH ILNMKLQWVC S DLPTYWASDLENQIKRS ACVMTLACHGGEMNGA LPQWRTHLLERTY KMN VVGGP ASSDALITGMQS DPILLVCATRGHEWAILF GHNLWA CVNMLETAIK L EGVFGSVLRAEKLNKAA PETYIN. . As with genomic sequence, we build computational filters that eliminate much of the database, leaving only a few candidates for the more expensive scoring.
Background image of page 8
Fa 06 CSE182 Basic Filtering Typical tools score all peptides with close enough parent mass and  tryptic termini Filtering by parent mass is problematic when PTMs are allowed, as  one must consider multiple parent masses
Background image of page 9

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Fa 06 CSE182 Tag-based filtering A tag is a short peptide with a prefix and suffix mass
Background image of page 10
Image of page 11
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 02/14/2008 for the course CSE 182 taught by Professor Bafna during the Fall '06 term at UCSD.

Page1 / 49

Lect13 Quantitation and other applications - CSE182-L13...

This preview shows document pages 1 - 11. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online