Get Started

pip install pept3

To get to know pept3, follow the next section to run a demo data.

Set up locally

clone this repo with:

git clone https://github.com/gusye1234/pept3.git
# fetch the pre-trained model weights:
git lfs install
git lfs pull
# install pept3 to python environment
pip install -e .

# run pept3 like an installed command
pept3 ./examples/demo_data/demo_input.tab --spmodel=prosit --similarity=SA --output_tab=./examples/demo_data/demo_out.tab --need_tensor --output_tensor=./examples/demo_data/tensor.hdf5

to perform a simple test-time training over Prosit(--spmodel=prosit) with Spectral Angle(--similarity=SA). The program will take ./examples/demo_data/demo_input.tab as the input file. Then the tuned features will be outputted to ./examples/demo_data/demo_out.tab, which is already for the downstream task, for example, as the input of the Percolator:

cd examples
bash ./percolator_demo.sh # rescoring over the tuned features set
# the result will be saved in ./examples/percolator_result

Also a python script for the above demo commands is available:

cd examples
python pept3_demo.py

You should get the identical result. The script pept3_demo.py will demonstrate the process of how PepT3 working inside python.

Input Format

PepT3 expects a tab-delimited file format as the input, just like Percolator. Each row should contains features associated with a single PSM:

SpecId <tab> Label <tab> ScanNr <tab> peak_ions <tab> peak_inten <tab> ... Charge <tab> <tab> Peptide <tab>

For PepT3, the input tab file should at least include those fields:

• SpecId(any type): Unique id for each PSM.
• ScanNr(any type): Same meaning as the Percolator.
• Label({1, -1}): 1 for target PSM, -1 for decoys.
• peak_ions: ;-delimited matched ions for PSM, only b/y types are considered currently. For example b10;b2;b3;
• peak_inten: Corresponding ions' intensities for the matched ions, also ;-delimited. For example 829;4154;168;
• Charge(int):, Percursor Charge
• collision_energy_aligned_normed(float, [0,1]): Maximun-normalized NCE.
• Peptides(str)

For the input example, have a look at ./examples/demo_data/demo_input.tab. Please note that: For any feature that not on the above list, PepT3 will automaticly merge it into the output tab

Output Format

PepT3 outputs a tab-delimited file format with each row contains enlarged features associated with a single PSM. The output tab file can be directly used as the input of the Percolator. Have a look at each features meaning in ./FEATURES.txt. Also, for those who want to visit the tuned spectrum prediction, use --need_tensor option and set --output_tensor. The prediction will be store as the format of hfd5, with columns SpecId and tuned-tensor. For the output example, please have a look at ./examples/demo_data/demo_out.tab and ./examples/demo_data/tensor.hdf5