# Proteomics Introductions

There is a recent tutorial by 
[Steven Shuken (2023) on massspetrometry-based proteomics](https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00838), I enjoyed reading.

Lennart Martens has an introduction to Proteomics [lecture series on youtube](https://www.youtube.com/watch?v=Wy1SwrMzhYk&list=PLXxp6nsBenSX_W8DiOocKJ0laNauYNdYl) 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](https://www.youtube.com/watch?v=tnS-w8ggEAA&list=PL_6fafgzU1nHd13qqjm3uNvyHh62JpPcB&index=2&t=0s).

## Pipeline 
Graphical overview of the Data Dependent Analysis (DDA) pipeline.

![Proteomics Pipeline](Figures/fig_proteomics_pipeline.png)

### Orbitrap
Schematic representation of an Orbitrap mass spectrometer.
![Schema Orbitrap](Figures/schema_orbitrap_instrument.jpg)

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