biosaur2

A feature detection LC-MS1 spectra.

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View statistics for this project via Libraries.io, or by using our public dataset on Google BigQuery

Project description

biosaur2 - A feature detection LC-MS1 spectra. This project is a rewriten version of Biosaur software (https://github.com/abdrakhimov1/Biosaur).

The centroided mzML file is required for of the script.

Algorithm can be run with following command:

biosaur2 path_to_MZML

The script output contains tsv table with peptide features.

All available arguments can be shown with command "biosaur2 -h".

The default parameter minlh (the minimal number of consecutive scans for peptide feature) is 1 and this value is optimimal for ultra-short LC gradients (a few minutes). For the longer LC gradients, this value can be increased for reducing of feature detection time and removing noise isotopic clusters.

For TOF data please add "-tof" argument.

For PASEF data please convert mzML file using msconvert and '--combineIonMobilitySpectra --filter "msLevel 1" ' options. Do not use option --filter "scanSumming"! The latter is often required for MS/MS data analysis but breaks MS1 feature detection.

For negative mode data please add "-nm" argument.

Citing biosaur2

Abdrakhimov, et al. Biosaur: An open-source Python software for liquid chromatography-mass spectrometry peptide feature detection with ion mobility support. https://doi.org/10.1002/rcm.9045

Installation

Using the pip:

pip install biosaur2

Project details

These details have not been verified by PyPI

View statistics for this project via Libraries.io, or by using our public dataset on Google BigQuery

Release history Release notifications | RSS feed

0.2.213 yanked

May 21, 2024

0.2.23

May 23, 2024

0.2.22

May 21, 2024

0.2.16

Aug 14, 2023

0.2.15

Aug 14, 2023

0.2.11

Jan 31, 2023

0.2.9

Dec 7, 2022

0.2.7

Oct 24, 2022

0.2.6

Oct 11, 2022

This version

0.2.3

Aug 17, 2022

0.2.1

Jun 21, 2022

0.1.9.2

May 13, 2022

0.1.9.1

May 13, 2022

0.1.9

Apr 28, 2022

0.1.8

Apr 26, 2022

0.1.7

Apr 5, 2022

0.1.6

Mar 10, 2022

0.1.5

Mar 9, 2022

0.1.4

Mar 2, 2022

0.1.3

Feb 21, 2022

0.1.2

Feb 21, 2022

0.1.1

Feb 21, 2022

0.1.0

Feb 18, 2022

0.0.9

Feb 17, 2022

0.0.7

Jan 20, 2022

0.0.6

Dec 17, 2021

0.0.5

Nov 24, 2021

0.0.4

Nov 24, 2021

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Source Distribution

biosaur2-0.2.3.tar.gz (148.9 kB view hashes)

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Built Distributions

biosaur2-0.2.3-cp310-cp310-win_amd64.whl (120.2 kB view hashes)

Uploaded Aug 17, 2022 CPython 3.10 Windows x86-64

biosaur2-0.2.3-cp310-cp310-musllinux_1_1_x86_64.whl (859.8 kB view hashes)

Uploaded Aug 17, 2022 CPython 3.10 musllinux: musl 1.1+ x86-64

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biosaur2-0.2.3-cp38-cp38-win_amd64.whl (121.5 kB view hashes)

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biosaur2-0.2.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (841.5 kB view hashes)

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Hashes for biosaur2-0.2.3.tar.gz

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