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Merge pull request #15 from MannLabs/development
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EugeniaVoytik committed Mar 18, 2022
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2 changes: 1 addition & 1 deletion .gitattributes
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.ipynb linguist-documentation
*.ipynb linguist-language=Python
7 changes: 7 additions & 0 deletions HISTORY.md
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## Changelog

### 1.1.0
* FEAT: Integrate the AlphaPeptDeep package into AlphaViz to predict the peptide properties, such as the MS2 intensity prediction for DDA data and retention time/ion mobility prediction for DIA data.
* FEAT: Update the Quality Control tab to make it lighter than the previous version. Variables for plots (m/z, im, rt, length, etc. distributions) can now be selected.
* FEAT: Reorganize the Settings panel and add more customization options.
* DOCS: Extend Jupyter notebooks for manual visual inspection of timsTOF DDA and DIA data analyzed by MaxQuant and DIA-NN, respectively.


### 1.0.5

* FEAT: Enable the possibility to read DIA data analysed by the DIA-NN software analysis tool.
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7 changes: 3 additions & 4 deletions README.md
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[![Downloads](https://pepy.tech/badge/alphaviz)](https://pepy.tech/project/alphaviz)
[![Downloads](https://pepy.tech/badge/alphaviz/month)](https://pepy.tech/project/alphaviz)
[![Downloads](https://pepy.tech/badge/alphaviz/week)](https://pepy.tech/project/alphaviz)
[![Documentation Status](https://readthedocs.org/projects/alphaviz/badge/?version=latest)](https://alphaviz.readthedocs.io/en/latest/?badge=latest)


# AlphaViz
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Software tools such as **MaxQuant** or **DIA-NN** identify and quantify high amounts of proteins. After downstream processing in **Perseus**, **MSstats** or the **Clinical Knowledge Graph**, differentially expressed proteins become possible candidates for biomarker discovery. **AlphaViz** is an automated visualization pipeline to link these identifications with the original raw data and easily assess their individual quality or the overall quality whole samples.

Data that was processed by any of the above-mentioned software tools can be uploaded to **AlphaViz** and proteins of interests can be selected to explore all available information about the identified peptides. It shows the position of each peptide on the protein sequence, its extracted ion chromatogram or the spectra with the identified b- or y-ions. Additionally, it visualizes the position where the precursor was peaked for sequencing on MS1 and MS2/PASEF frames.

An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann). This project is built purely in Python using a new cutting-edge [Holoviz ecosystem](https://holoviz.org/index.html) and Plotly library to create interactive dashboards and plots.

---
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AlphaViz can be imported as a Python package into any Python script or notebook with the command `import alphaviz`.

A brief Jupyter notebook tutorial on how to use the API will be added soon.
An ‘nbs’ folder in the GitHub repository contains several Jupyter Notebooks as tutorials regarding using AlphaViz as a Python package for all available pipelines: for DDA data analyzed with MaxQuant, for DIA data analyzed with DIA-NN, and for the targeted mode.

---
## Troubleshooting
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---
## Citations

There are currently no plans to draft a manuscript.
A manuscript is currently in preparation.

---
## How to contribute
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2 changes: 1 addition & 1 deletion alphaviz/__init__.py
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#!python

__project__ = "alphaviz"
__version__ = "1.0.5"
__version__ = "1.1.0"
__license__ = "Apache"
__description__ = "A interactive Dashboard to explore mass spectrometry data."
__author__ = "Eugenia Voytik"
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66 changes: 33 additions & 33 deletions alphaviz/data/modifications.tsv
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Description Type Amino Acid Residue Monoisotopic Mass Shift (Da) Average Mass Shift (Da) Monoisotopic Neutral Loss Mass (Da) Average Neutral Loss Mass (Da) Default UniMod Accession Number UniMod Name Notes Identifier
carbamidomethylation of C amino acid residue C 57.02146373 57.05132 0 0 fixed 4 Carbamidomethyl CH3NO cC
oxidation of M amino acid residue M 15.99491463 15.9994 0 0 variable 35 Oxidation O oxM
acetylation of protein N-terminus protein N-terminus N 42.01056469 42.03668 0 0 none 1 Acetyl C2H2O a<^
amidation of protein C-terminus protein C-terminus N -0.984015593 -0.98476 0 0 none 2 amidated H-1N-1O am>^
acetylation of lysine amino acid residue K 42.01056469 42.03668 0 0 none 1 Acetyl C2H2O aK
phosphorylation of S amino acid residue S 79.96633092 79.979902 0 0 none 21 Phospho HPO3 pS
phosphorylation of T amino acid residue T 79.96633092 79.979902 0 0 none 21 Phospho HPO3 pT
phosphorylation of Y amino acid residue Y 79.96633092 79.979902 0 0 none 21 Phospho HPO3 pY
deamidation of N amino acid residue N 0.984015593 0.98476 0 0 none 7 Deamidated H-1N-1O deamN
deamidation of Q amino acid residue Q 0.984015593 0.98476 0 0 none 7 Deamidated H-1N-1O deamNQ
pyro-cmC peptide N-terminus C -17.0265491 -17.03052 0 0 none 26 Pyro-carbamidomethyl H-3N-1 cm<C
pyro-E peptide N-terminus E -18.01056469 -18.01528 0 0 none 27 Glu->pyro-Glu H-2O-1 pg<E
pyro-Q peptide N-terminus Q -17.0265491 -17.03052 0 0 none 28 Gln->pyro-Glu H-3N-1 pg<Q
TMT zero on peptide N-terminus peptide N-terminus N 224.1524779 224.2994 0 0 none 739 TMT C12H20N2O2 tmt0<^
TMT zero on K amino acid residue K 224.1524779 224.2994 0 0 none 739 TMT C12H20N2O2 tmt0K
TMT zero on Y amino acid residue Y 224.1524779 224.2994 0 0 none 739 TMT C12H20N2O2 tmt0Y
TMT duplex on peptide N-terminus peptide N-terminus N 225.1558328 225.2920548 0 0 none 738 TMT2plex C11(13C)H20N2O2 tmt2<^
TMT duplex on K amino acid residue K 225.1558328 225.2920548 0 0 none 738 TMT2plex C11(13C)H20N2O2 tmt2K
TMT duplex on Y amino acid residue Y 225.1558328 225.2920548 0 0 none 738 TMT2plex C11(13C)H20N2O2 tmt2Y
TMT sixplex/tenplex on peptide N-terminus peptide N-terminus N 229.1629322 229.2634282 0 0 none 737 TMT6plex C8(13C)4H20N(15N)O2 tmt6<^
TMT sixplex/tenplex on K amino acid residue K 229.1629322 229.2634282 0 0 none 737 TMT6plex C8(13C)4H20N(15N)O2 tmt6K
TMT sixplex/tenplex on Y amino acid residue Y 229.1629322 229.2634282 0 0 none 737 TMT6plex C8(13C)4H20N(15N)O2 tmt6Y
iTRAQ 4-plex on peptide N-terminus peptide N-terminus N 144.1024104 144.1613902 0 0 none 214 iTRAQ 114:C5(13C)2H12N2(18O) + 115:C6(13C)H12N(15N)(18O) + 116/117:C4(13C)3H12N(15N)O itraq4K<^
iTRAQ 4-plex on K amino acid residue K 144.1024104 144.1613902 0 0 none 214 iTRAQ 114:C5(13C)2H12N2(18O) + 115:C6(13C)H12N(15N)(18O) + 116/117:C4(13C)3H12N(15N)O itraq4K
iTRAQ 4-plex on Y amino acid residue Y 144.1024104 144.1613902 0 0 none 214 iTRAQ 114:C5(13C)2H12N2(18O) + 115:C6(13C)H12N(15N)(18O) + 116/117:C4(13C)3H12N(15N)O itraq4Y
iTRAQ 8-plex on peptide N-terminus peptide N-terminus N 304.2021995 304.3077298 0 0 none 730 iTRAQ8plex 113/114/116/117:C7(13C)7H24N3(15N)O3 + 115/118/119/121:C8(13C)6H24N2(15N)2O3 itraq8K<^
iTRAQ 8-plex on K amino acid residue K 304.2021995 304.3077298 0 0 none 730 iTRAQ8plex 113/114/116/117:C7(13C)7H24N3(15N)O3 + 115/118/119/121:C8(13C)6H24N2(15N)2O3 itraq8K
iTRAQ 8-plex on Y amino acid residue Y 304.2021995 304.3077298 0 0 none 730 iTRAQ8plex 113/114/116/117:C7(13C)7H24N3(15N)O3 + 115/118/119/121:C8(13C)6H24N2(15N)2O3 itraq8Y
EASItag 6-plex on peptide N-terminus peptide N-terminus < 266.0838675 266.0838675 0 0 none 999999999 EASItag6plex 12C513C5H15O5NS e<^
EASItag 6-plex on K amino acid residue K 266.0838675 266.0838675 0 0 none 999999999 EASItag6plex 12C513C5H15O5NS eK
Arg 10 on peptide C-terminus peptide C-terminus R 10.008269577760007 10.008269577760007 0 0 none none Arg10 13C615N4 arg10>R
Arg 6 on peptide C-terminus peptide C-terminus R 6.020130000000005 6.020130000000005 0 0 none none Arg6 13C6 arg6>R
Description Type Amino Acid Residue Monoisotopic Mass Shift (Da) Average Mass Shift (Da) Monoisotopic Neutral Loss Mass (Da) Average Neutral Loss Mass (Da) Default UniMod Accession Number UniMod Name Notes Identifier
carbamidomethylation of C amino acid residue C 57.02146373 57.05132 0 0 fixed 4 Carbamidomethyl CH3NO cC
oxidation of M amino acid residue M 15.99491463 15.9994 0 0 variable 35 Oxidation O oxM
acetylation of protein N-terminus protein N-terminus N 42.01056469 42.03668 0 0 none 1 Acetyl C2H2O a<^
amidation of protein C-terminus protein C-terminus N -0.984015593 -0.98476 0 0 none 2 amidated H-1N-1O am>^
acetylation of lysine amino acid residue K 42.01056469 42.03668 0 0 none 1 Acetyl C2H2O aK
phosphorylation of S amino acid residue S 79.96633092 79.979902 0 0 none 21 Phospho HPO3 pS
phosphorylation of T amino acid residue T 79.96633092 79.979902 0 0 none 21 Phospho HPO3 pT
phosphorylation of Y amino acid residue Y 79.96633092 79.979902 0 0 none 21 Phospho HPO3 pY
deamidation of N amino acid residue N 0.984015593 0.98476 0 0 none 7 Deamidated H-1N-1O deamN
deamidation of Q amino acid residue Q 0.984015593 0.98476 0 0 none 7 Deamidated H-1N-1O deamNQ
pyro-cmC peptide N-terminus C -17.0265491 -17.03052 0 0 none 26 Pyro-carbamidomethyl H-3N-1 cm<C
pyro-E peptide N-terminus E -18.01056469 -18.01528 0 0 none 27 Glu->pyro-Glu H-2O-1 pg<E
pyro-Q peptide N-terminus Q -17.0265491 -17.03052 0 0 none 28 Gln->pyro-Glu H-3N-1 pg<Q
TMT zero on peptide N-terminus peptide N-terminus N 224.1524779 224.2994 0 0 none 739 TMT C12H20N2O2 tmt0<^
TMT zero on K amino acid residue K 224.1524779 224.2994 0 0 none 739 TMT C12H20N2O2 tmt0K
TMT zero on Y amino acid residue Y 224.1524779 224.2994 0 0 none 739 TMT C12H20N2O2 tmt0Y
TMT duplex on peptide N-terminus peptide N-terminus N 225.1558328 225.2920548 0 0 none 738 TMT2plex C11(13C)H20N2O2 tmt2<^
TMT duplex on K amino acid residue K 225.1558328 225.2920548 0 0 none 738 TMT2plex C11(13C)H20N2O2 tmt2K
TMT duplex on Y amino acid residue Y 225.1558328 225.2920548 0 0 none 738 TMT2plex C11(13C)H20N2O2 tmt2Y
TMT sixplex/tenplex on peptide N-terminus peptide N-terminus N 229.1629322 229.2634282 0 0 none 737 TMT6plex C8(13C)4H20N(15N)O2 tmt6<^
TMT sixplex/tenplex on K amino acid residue K 229.1629322 229.2634282 0 0 none 737 TMT6plex C8(13C)4H20N(15N)O2 tmt6K
TMT sixplex/tenplex on Y amino acid residue Y 229.1629322 229.2634282 0 0 none 737 TMT6plex C8(13C)4H20N(15N)O2 tmt6Y
iTRAQ 4-plex on peptide N-terminus peptide N-terminus N 144.1024104 144.1613902 0 0 none 214 iTRAQ 114:C5(13C)2H12N2(18O) + 115:C6(13C)H12N(15N)(18O) + 116/117:C4(13C)3H12N(15N)O itraq4K<^
iTRAQ 4-plex on K amino acid residue K 144.1024104 144.1613902 0 0 none 214 iTRAQ 114:C5(13C)2H12N2(18O) + 115:C6(13C)H12N(15N)(18O) + 116/117:C4(13C)3H12N(15N)O itraq4K
iTRAQ 4-plex on Y amino acid residue Y 144.1024104 144.1613902 0 0 none 214 iTRAQ 114:C5(13C)2H12N2(18O) + 115:C6(13C)H12N(15N)(18O) + 116/117:C4(13C)3H12N(15N)O itraq4Y
iTRAQ 8-plex on peptide N-terminus peptide N-terminus N 304.2021995 304.3077298 0 0 none 730 iTRAQ8plex 113/114/116/117:C7(13C)7H24N3(15N)O3 + 115/118/119/121:C8(13C)6H24N2(15N)2O3 itraq8K<^
iTRAQ 8-plex on K amino acid residue K 304.2021995 304.3077298 0 0 none 730 iTRAQ8plex 113/114/116/117:C7(13C)7H24N3(15N)O3 + 115/118/119/121:C8(13C)6H24N2(15N)2O3 itraq8K
iTRAQ 8-plex on Y amino acid residue Y 304.2021995 304.3077298 0 0 none 730 iTRAQ8plex 113/114/116/117:C7(13C)7H24N3(15N)O3 + 115/118/119/121:C8(13C)6H24N2(15N)2O3 itraq8Y
EASItag 6-plex on peptide N-terminus peptide N-terminus < 266.0838675 266.0838675 0 0 none 999999999 EASItag6plex 12C513C5H15O5NS e<^
EASItag 6-plex on K amino acid residue K 266.0838675 266.0838675 0 0 none 999999999 EASItag6plex 12C513C5H15O5NS eK
Arg 10 on peptide C-terminus peptide C-terminus R 10.008269577760007 10.008269577760007 0 0 none none Arg10 13C615N4 arg10>R
Arg 6 on peptide C-terminus peptide C-terminus R 6.020130000000005 6.020130000000005 0 0 none none Arg6 13C6 arg6>R
Lys 8 on peptide C-terminus peptide C-terminus K 8.014199788880006 8.014199788880006 0 0 none none Lys8 13C15N2 lys8>K
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