SIMSI-Transfer
Transferring identifications using MS2 spectrum clustering with MaxQuant search results.
Hamood, F., Bayer, F. P., Wilhelm, M., Kuster, B., & The, M. (2022). SIMSI-Transfer: Software-assisted reduction of missing values in phosphoproteomic and proteomic isobaric labeling data using tandem mass spectrum clustering. Molecular & Cellular Proteomics, 100238.
Test dataset
For testing SIMSI-Transfer after installation, we recommend downloading the TMT11 MS2 raw files from this publication: Thompson, A., Wölmer, N., Koncarevic, S., Selzer, S. et al., TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set. Analytical Chemistry 2019, 91, 15941–15950. doi:10.1021/acs.analchem.9b04474
PRIDE link: https://www.ebi.ac.uk/pride/archive/projects/PXD014750
Raw files for TMT-MS2:
- 19070-001.raw
- 19070-002.raw
- 19070-003.raw
- 19070-006.raw
- 19070-007.raw
- 19070-008.raw
The MaxQuant results needed as input to SIMSI-Transfer can be downloaded from Zenodo:
For reference, the original SIMSI-Transfer results (v0.1.0) for this dataset can also be downloaded from Zenodo:
Running SIMSI-Transfer using the GUI
On Windows, you can download the SIMSI-Transfer_GUI_windows.zip from the latest release, unzip it and open SIMSI-Transfer.exe to start the GUI (no installation necessary).
Alternatively, on all platforms, first install SIMSI-Transfer as explained below. Then install PyQt5 (pip install PyQt5) and run:
python gui.py
Running SIMSI-Transfer from the command line
First install SIMSI-Transfer as explained below, then run SIMSI-Transfer:
python -m simsi_transfer --mq_txt_folder </path/to/txt/folder> --raw_folder </path/to/raw/folder> --output_folder </path/to/output/folder>
Alternative command for MS3 acquisition, using the TMT correction factor file exported from MaxQuant:
python -m simsi_transfer --mq_txt_folder </path/to/txt/folder> --raw_folder </path/to/raw/folder> --output_folder </path/to/output/folder> --tmt_ms_level ms3 --tmt_requantify --tmt_reporter_correction_file </path/to/correction/factor/file.txt>
Alternative command using the meta input file for MS3 acquisition, with filtered decoys:
python -m simsi_transfer --meta_input_file </path/to/meta/file> --output_folder </path/to/output/folder> --tmt_ms_level ms3 --tmt_requantify --filter_decoys
A list of all possible arguments is displayed using the help argument:
python -m simsi_transfer --help
Installation
SIMSI-Transfer is available on PyPI and can be installed with pip:
pip install simsi-transfer
Alternatively, you can install SIMSI-Transfer after cloning from this repository:
git clone https://github.com/kusterlab/SIMSI-Transfer.git
pip install .
2 maintainers
Metadata
2 maintainers
Release files for simsi-transfer 0.8.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| simsi_transfer-0.8.0.tar.gz | 7.7 MB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| simsi_transfer-0.8.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 15.4 MB
Release files / simsi_transfer-0.8.0.tar.gz
| Download URL | simsi_transfer-0.8.0.tar.gz |
|---|---|
| Size | 7.7 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
e87ef7592bc118df892b4ad16a5a1934a70166a0df16e7754593115325de5b6f
|
|
BLAKE2b-256 checksum How to use checksums |
ac3c0432862538559f4f5fd2ecb1b67693ca09a9161778dbaeb78c45f7da9051
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.9.23
|
Release files / simsi_transfer-0.8.0-py3-none-any.whl
| Download URL | simsi_transfer-0.8.0-py3-none-any.whl |
|---|---|
| Size | 7.8 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
be54b8ef0218b22de57b2b90f3cb9d65f55d75eb34b47d12bec37003e8be0561
|
|
BLAKE2b-256 checksum How to use checksums |
f6bc719cde2d11178afdafb9623a89257c629a9f79988a3a05d5ea2fa03c7ece
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.9.23
|
Security for simsi-transfer 0.8.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
