L21 Bioinformatics III - Identification of proteins

what is genomics used to find out

what could the cell do

what is transcriptomics used to find out

what intends the cell to do something

what is proteomics used to find out

what the cell is actually doing

what is metabolomics used to find out

what did the cell do

how many genes are spliced in genomics

20000 (10000 genes/cell)

how many transcripts are given post-translational modifications in transcriptomics

100,000

how many proteic forms form metabolomics from proteomics

10^5 - 10^6

give examples of some mass spectrometres

• LTQ orbitrap XL

• Q exactive

• MALDI TOF

• orbitrap fusion

• triple TOF

what will spectral lines never have

the exact same value

how is tolerance defined to solve the problem of spectral lines never having the exact same value

when a value is within the tolerance window of another value, algorithms consider them equal

since in MSMS there are 2 spectra, what 2 tolerances are needed

• precursor ion

• fragments

what is the tolerance of the precursor ion

limits the database to the peptides having the same mass

what is the tolerance of the fragments

determines which lines in the spectrum are used

either for technical or biological reasons, many peptides have…

post-translational modifications which affect their mass

what are fixed modifications

those affecting all the amino acids of the same type

give an example of fixed modifications

the carbamidomethylation of cysteine (57.02 Da)

give an example of variable modifications

the oxidation of methionine (15.99 Da)

what are variable modifications

those affecting part of the amino acids of the same type, but not all

what are the cells doing

they are busy taking glucose from the blood and storing it as glycogen via glycogenesis

overview of protein identification