10_06_BRAIN.Rmd

### BRAIN
**Baffling Recursive Algorithm for Isotope distributioN calculations**

R BRAIN is an isotopic abundance calculator implemented in R programming language and is especially useful for chemists and researchers who deal with complex molecules and need to calculate their isotopic composition accurately. In addition, it has a handy function for calculating the mass directly from an amino acid sequence.

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+---------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ![](images/05.png){height="68"} | [Bioconductor](https://bioconductor.org/packages/release/bioc/manuals/BRAIN/man/BRAIN.pdf)                                                                                            |
|                                 |                                                                                                                                                                                       |
|                                 | *Dittwald, Piotr, et al. "BRAIN: a universal tool for high-throughput calculations of the isotopic distribution for mass spectrometry." Analytical chemistry 85.4 (2013): 1991-1994.* |
+---------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

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#### Installation {-}
```{r, eval=FALSE}
BiocManager::install("BRAIN")
```

#### Useage {-}
```{r, message=FALSE, warning=FALSE}
library(BRAIN)

# Human insulin amino acid sequence
str_seq <- "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"

# get a list-object of atoms
lst_atm <- getAtomsFromSeq(str_seq) 
```

Calculate the average mass.
```{r}
calculateAverageMass(lst_atm)
```

Calculate the monoisotopic mass.
```{r}
calculateMonoisotopicMass(lst_atm)
```

Calculate the isotopic abundances (probabilities) mass.
```{r, fig.width=6, fig.height=3, fig.align='center'}
lst_isotopes <- useBRAIN(lst_atm, nrPeaks = 20)

plot(lst_isotopes$masses, lst_isotopes$isoDistr, xlab='Mass', ylab='Probability', type = 'h')
```
Calculate the isotopic abundances (probabilities) mass for a metabolite [C100H200S2Cl5].
```{r, fig.width=6, fig.height=3, fig.align='center'}

lst_atm <- list(C=100, H=200, S=2, Cl=5)

lst_isotopes <- useBRAIN(lst_atm, nrPeaks = 13)

plot(x = lst_isotopes$masses, 
     y = lst_isotopes$isoDistr / max(lst_isotopes$isoDistr) * 100, 
     xlab='Mass', ylab='Relative abundance', type = 'h')
```

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