NeoMS is an end-to-end immunopeptidomics data analysis tool. NeoMS takes raw data as input and return the search result with high quality. The main steps of NeoMS is compiled in Nextflow(https://www.nextflow.io/docs/latest/getstarted.html)
-
GPU is required to run NeoMS.
-
Install Nextflow 20.10 and add to environment variables.
-
Install docker. Tools used by NeoMS have been dockerized and will be automatically installed when NeoMS is run in the first time on a computer. NeoMS has been tested on Linux.
-
Download NeoMS from Github
git clone https://github.com/waterlooms/NeoMS.git
- Download test raw data in data folder
cd data/
chmod +x download_test.sh
bash download_test.sh
- Run the whole pipeline. The whole pipeline include 4 steps in nextflow:
- Preprocessing: Convert the raw file to mgf format.
- De novo: Run de novo software (Novor) on the mgf file and compute features on de novo PSMs(Peptide Spectrum Matching).
- Database search: Run database search tool (comet) on the mgf file and compute features on searched PSMs. Notice that the .fasta file will be copy to /tmp folder.
- Combine: Combine features from de novo and db search result. A machine learning model is applied to compute a score for each PSM.
The 4 steps have been put into single bash file. You can run the whole pipeline simply by:
chmod +x test.sh
bash test.sh
- It will automatically generate a folder in result/ with same name of raw file. It might take 30~40 mins for the whole pipeline. After finished, the result is at result/20120321_EXQ1_MiBa_SA_HCC1143_1/result.csv.
The result includes best peptide(can be target or decoy) for each spectrum. The result will be sorted by a score. The first few rows will be like this:
| index | charge | mass | peptide | mods | protein | myscore |
|---|---|---|---|---|---|---|
| 20120321_EXQ1_MiBa_SA_HCC1143_1.10327.10327.2 | 2 | 1122.541603 | SRSQNQQYL | 0 | sp|O14782|KIF3C_HUMAN,sp|O15066|KIF3B_HUMAN | 1.090571005 |
| 20120321_EXQ1_MiBa_SA_HCC1143_1.14812.14812.2 | 2 | 1073.514985 | QRYSGSTYL | 0 | sp|P54277|PMS1_HUMAN | 1.086924661 |
| 20120321_EXQ1_MiBa_SA_HCC1143_1.5907.5907.3 | 3 | 1096.653946 | RRAAQVQRL | 0 | sp|Q969G5|CAVN3_HUMAN | 1.071481355 |
| 20120321_EXQ1_MiBa_SA_HCC1143_1.2026.2026.3 | 3 | 1129.518549 | HRSPHTHQM | 0 | sp|P11230|ACHB_HUMAN | 1.064637078 |
| 20120321_EXQ1_MiBa_SA_HCC1143_1.23613.23613.2 | 2 | 1013.586828 | SRAELVQLV | 0 | sp|Q96ST3|SIN3A_HUMAN | 1.057023507 |