Merge pull request #3 from MannLabs/development

Development

.gitattributes

@@ -0,0 +1 @@
+.ipynb linguist-documentation

.github/workflows/publish_and_release.yml

@@ -1,6 +1,6 @@
 on:
-  # push:
-  #   branches: [ main ]
+  push:
+    branches: [ main ]
   workflow_dispatch:
 
 

HISTORY.md

@@ -1,5 +1,15 @@
 ## Changelog
 
+### 1.0.5
+
+* FEAT: Enable the possibility to read DIA data analysed by the DIA-NN software analysis tool.
+* FEAT: Extend the "Quality Control" tab with a summary statistics table and additional plots.
+* FEAT: Add a "Targeted Mode" tab to work with raw data only.
+* DOCS: Update the AlphaViz tutorial with all functionality implemented.
+* FEAT: Create detailed notebooks demonstrating visualisation of DDA and DIA data analysed with MaxQuant and DIA-NN respectively.
+* FIX: Correct the error when reading the MQ output files (missing columns).
+
 ### 0.0.1
 
 * FEAT: Initial creation of alphaviz.
+* FEAT: Read DDA Bruker data processed with MaxQuant software.

LICENSE.txt

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2021 MannLabs
+   Copyright 2022 MannLabs
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

README.md

@@ -6,7 +6,7 @@
 
 
 # AlphaViz
-**AlphaViz** is a cutting-edge browser-based interactive visualization tool allowing to visualize the processed mass spectrometry data acquired with **Bruker** or **Thermo** instruments. The **AlphaViz** dashboard facilitates easy quality control of your analyzed samples and a clear inspection of the raw data of significant peptides/proteins.
+**AlphaViz** is a cutting-edge browser-based interactive visualization tool allowing to visualize the processed mass spectrometry data acquired with **Bruker** instrument. The **AlphaViz** dashboard facilitates easy quality control of your analyzed samples and a clear inspection of the raw data of significant peptides/proteins.
 
 To enable all hyperlinks in this document, please view it at [GitHub](https://github.com/MannLabs/alphaviz).
 
@@ -28,7 +28,7 @@ To enable all hyperlinks in this document, please view it at [GitHub](https://gi
 ---
 ## About
 
-Software tools such as **AlphaPept**, **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.
+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.
 
@@ -42,7 +42,7 @@ AlphaViz was developed by the [Mann Labs at the Max Planck Institute of Biochemi
 ---
 ## Installation
 
-AlphaViz can be installed and used on all major operating systems (Windows, macOS). (*) Linux will be included soon.
+AlphaViz can be installed and used on all major operating systems (Windows, macOS, Linux).
 There are three different types of installation possible:
 
 * [**One-click GUI installer:**](#one-click-gui) Choose this installation if you only want the GUI and/or keep things as simple as possible.
@@ -72,7 +72,7 @@ pip install alphaviz
 Installing AlphaViz like this avoids conflicts when integrating it in other tools, as this does not enforce strict versioning of dependancies. However, if new versions of dependancies are released, they are not guaranteed to be fully compatible with AlphaViz. While this should only occur in rare cases where dependencies are not backwards compatible, you can always force AlphaViz to use dependancy versions which are known to be compatible with:
 
 ```bash
-pip install "alphaviz[stable]"
+pip install "alphaviz[gui-stable]"
 ```
 
 NOTE: You might need to run `pip install pip==21.0` before installing alphaviz like this. Also note the double quotes `"`.
@@ -131,7 +131,7 @@ NOTE: The first time you use a fresh installation of AlphaViz, it is often quite
 If the GUI was not installed through a one-click GUI installer, it can be activate with the following `bash` command:
 
 ```bash
-alphaviz
+alphaviz gui
 ```
 
 Note that this needs to be prepended with a `!` when you want to run this from within a Jupyter notebook. When the command is run directly from the command-line, make sure you use the right environment (activate it with e.g. `conda activate alphaviz` or set an alias to the binary executable (can be obtained with `where alphaviz` or `which alphaviz`)).

alphaviz/__init__.py

@@ -1,7 +1,7 @@
 #!python
 
 __project__ = "alphaviz"
-__version__ = "0.0.2"
+__version__ = "1.0.5"
 __license__ = "Apache"
 __description__ = "A interactive Dashboard to explore mass spectrometry data."
 __author__ = "Eugenia Voytik"
@@ -20,8 +20,8 @@
 __classifiers__ = [
         # "Development Status :: 1 - Planning",
         # "Development Status :: 2 - Pre-Alpha",
-        "Development Status :: 3 - Alpha",
-        # "Development Status :: 4 - Beta",
+        # "Development Status :: 3 - Alpha",
+        "Development Status :: 4 - Beta",
         # "Development Status :: 5 - Production/Stable",
         # "Development Status :: 6 - Mature",
         # "Development Status :: 7 - Inactive"

alphaviz/data/amino_acids.tsv

@@ -0,0 +1,22 @@
+Identifier	Monoisotopic Mass (Da)	Average Mass (Da)	Notes
+A	71.0371138	71.0779	alanine, Ala, C3H5NO
+C	103.0091845	103.1429	cysteine, Cys, C3H6NOS
+D	115.0269431	115.0874	aspartic acid, Asp, C4H5NO3
+E	129.0425931	129.11398	glutamic acid, Glu, C5H7NO3
+F	147.0684139	147.17386	phenylalanine, Phe, C9H9NO
+G	57.02146373	57.05132	glycine, Gly, C2H3NO
+H	137.0589119	137.13928	histidine, His, C6H7N3O
+I	113.084064	113.15764	isoleucine, Ile, C6H11NO
+K	128.094963	128.17228	lysine, Lys, C6H12N2O
+L	113.084064	113.15764	leucine, Leu, C6H11NO
+M	131.0404846	131.19606	methionine, Met, C5H9NOS
+N	114.0429275	114.10264	asparagine, Asn, C4H6N2O2
+P	97.05276386	97.11518	proline, Pro, C5H7NO
+Q	128.0585775	128.12922	glutamine, Gln, C5H8N2O2
+R	156.101111	156.18568	arginine, Arg, C6H12N4O
+S	87.03202843	87.0773	serine, Ser, C3H5NO2
+T	101.0476785	101.10388	threonine, Thr, C4H7NO2
+U	150.9536333957	150.0379	selenocysteine, SeC, C3H5NOSe
+V	99.06841392	99.13106	valine, Val, C5H9NO
+W	186.079313	186.2099	tryptophan, Trp, C11H10N2O
+Y	163.0633286	163.17326	tyrosine, Try, C9H9NO2

alphaviz/data/modifications.tsv

@@ -0,0 +1,34 @@
+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