---
title: "Playng with Proteomics pt. 2"
output: html_notebook
---

Having obtained converted .mzXML files, we can now start trying to get Comet, TPP, and PECAN to work. First we're going to run comet, making sure that our params file and the reference proteome is in the same directory as the mzXML files. 

```{r}
setwd("~/Documents/mzMXL_files/")

system("/home/shared/comet/comet.2016012.linux.exe -Pcomet.params.high-low -Dgigas-proteome.fasta *.mzXML")
```


```{r}
filelist <- list.files(path = "~/Documents/mzMXL_files", pattern = "*.pep.xml")

for(i in 1:length(filelist))   {
  print(paste("/usr/tpp_install/tpp/bin/xinteract", gsub(".pep.xml", "", filelist[i]), " -N", filelist[i], " -p0.9 -OAp -dDECOY_"))
}
```
