Proteomics Introductions#
There is a recent tutorial by Steven Shuken (2023) on massspetrometry-based proteomics, I enjoyed reading.
Lennart Martens has an introduction to Proteomics lecture series on youtube from 2016, which I watched to get started.
An introduction I have seen live in 2020 was from the OpenMS team from Tübingen at the EuBICs developer meeting in Nyborg, where you can find the recordings on youtube.
Pipeline#
Graphical overview of the Data Dependent Analysis (DDA) pipeline.
Orbitrap#
Schematic representation of an Orbitrap mass spectrometer.
Missing terms in the figure:
Term |
meaning |
|---|---|
c-Trap |
collects one million particles before forwarding them to the Orbitrap |
HCD |
Higher-energy collisional dissociation (MS2 fragmentation of MS1 ions) |
Amino Acids and residuals#
A table for reference.
Name |
abr |
code |
Residue Mass |
|---|---|---|---|
Alanine |
Ala |
A |
71.03711 |
Arginine |
Arg |
R |
156.10111 |
Aspartic Acid |
Asn |
N |
114.04293 |
Cysteine |
Cys |
C |
103.00919 |
Glutamic Acid |
Glu |
E |
129.04259 |
Glutamine |
Gln |
Q |
128.05858 |
Glycine |
Gly |
G |
57.02146 |
Histidine |
His |
H |
137.05891 |
Isoleucine |
Ile |
I |
113.08406 |
Leucine |
Leu |
L |
113.08406 |
Lysine |
Lys |
K |
128.09496 |
Methionine |
Met |
M |
131.04049 |
Phenyalanine |
Phe |
F |
147.06841 |
Proline |
Pro |
P |
97.05276 |
Serine |
Ser |
S |
87.03203 |
Threonine |
Thr |
T |
101.04768 |
Trypthophan |
Trp |
W |
186.07931 |
Tyrosine |
Tyr |
Y |
163.06333 |
Valine |
Val |
V |
99.06841 |