Download Assignment 02 Computational Proteomics and Metabolomics

Dr. Sven Nahnsen
Timo Sachsenberg
Mathias Walzer
Mathematisch-Naturwissenschaftliche Fakultät
Abteilung für Simulation biologischer Systeme
Zentrum für Bioinformatik Tübingen
Assignment 02
Computational Proteomics and Metabolomics
Masses and isotopes
hand in: [email protected]
Task II (a) monoisotopic, average and nominal mass:
Calculate the monoisotopic, average and nominal mass of the residue serine C3 H5 N O2 .
What is its mass defect/mass excess of serine?
element
H
H
C
C
N
N
O
O
O
mass
1.0078
2.0141
12.0000
13.0034
14.0031
15.0001
15.9949
16.9991
17.9992
rel. abundance
99.9885
0.0115
98.93
1.07
99.632
0.368
99.757
0.038
0.205
Which OpenMS method is used to calculate the monoisotopic and average mass for chemical formulas?
Which is used for sequences of amino acids?
(b) Da, amu and ppm:
Suppose the mass of a protein is measured to 18500 Da, with an uncertainty of 10 Da.
What is the uncertainty in mmu and ppm?
(c) isoelectric point (pI):
Consider the peptide EVEDLQVR.
Show that the theoretical pI value is between 4 and 4.5 .
Use the programs ’ProtParam’ and ’Compute pI/Mw’ from the expasy website to verify this.
(d) m/z ratio:
In a spectrogram there are two peaks at m/z values 239 and 358.
Examine if these can come from the same peptide, but with different charges and determine the charges in that
case.
(e) resolution (FWHM):
Suppose that a resolution of 7000 is obtained for peaks at m/z = 300.
What is the maximum charge at which isotopic resolution can still be obtained?
Download the file Assignment02 MSMap which has been generated on a modern mass spectrometer.
Open it in TOPPView and try to roughly estimate the resolution at m/z = 450.
(f) chromatograms:
Find approximate values for the necessary parameters, and calculate plate numbers, asymmetry factors, and
tailing factors for the two highest peaks.
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