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Status of code

Master

pipeline status coverage report

Develop

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Prosit gRPC Client as a poetry package

1. Simple installation by pip

We provide tagged versions of our package pointing to the latest tested master releases but can give you also direct access to new features if requested. The correctness is indicated by the green=good or red=wrong flags above.

pip install -e git+https://gitlab.lrz.de/proteomics/prosit_tools/[email protected]#egg=prosit_grpc

If you deployed an ssh key

pip install -e [email protected]:proteomics/prosit_tools/[email protected]#egg=prosit_grpc

2. Ask us for certificates

You are using a special access to our GPUs and are therefore required to identify against our server. We will provide you with certificates that are valid for a limited time but can be renewed. Do not share those certificates with people outside of our group.

3. How to use the gRPC Client using Python?

import

from prosit_grpc.predictPROSIT import PROSITpredictor

establish connection to server

predictor = PROSITpredictor(server="proteomicsdb.org:8500",
                            path_to_ca_certificate= "path/to/certificate/Proteomicsdb-Prosit-v2.crt",
                            path_to_certificate= "path/to/certificate/individual_certificate_name.crt",
                            path_to_key_certificate= "path/to/certificate/individual_certificate_name.key",
                            )

Write HDF5 == Get everything as file -> Input for any kind of converter

predictor.predict_to_hdf5(sequences=["AAAAAKAK","AAAAAA"],
                          charges=[1,2],
                          collision_energies=[25,25],
                          intensity_model="Prosit_2019_intensity",
                          irt_model="Prosit_2019_irt",
                          path_hdf5="output.hdf5")

Alternative: get predictions as dictionary in python

Predictions are generated for the model you specify.

# predicts intensity, proteotypicity, iRT
output_dict = predictor.predict(sequences=["AAAAAKAK","AAAAAA"],
                                charges=[1,2],
                                collision_energies=[25,25],
                                models=["Prosit_2019_intensity", "Prosit_2019_irt", "Prosit_2020_proteotypicity"])

Sequence Restrictions

The peptide Sequence can only contain the following AA abbreviations: (Cysteine is expected to be alkylated as such all three representations are treated the same)

Amino acid|accepted abbreviation

:-----:|:-----: Alanine|A Cysteine|C Aspartic acid|D Glutamic acid|E Phenylalanine|F Glycine|G Histidine|H Isoleucine|I Lysine|K Leucine|L Methionine|M Asparagine|N Proline|P Glutamine|Q Arginine|R Serine|S Threonine|T Valine|V Tryptophan|W Tyrosine|Y

Modified AA can be specified with:

Modified Amino Acid accepted abbreviation
Carbamidomethylated Cystein C(U:4)
Oxidized Methionine M(U:35)

Developer information

How to use the gRPC client in my own project using the poetry package managment system?

Specify the "SSH clone link" of the prosit_grpc repository in your pyproject.toml.

prosit_grpc = {git = "[email protected]:wilhelm-lab/prosit_grpc.git", rev = "main"}