Add introduction of a few concepts #39

tapaswenipathak · 2022-05-26T05:18:48Z

Fixes #14.

Describe the change

Ref: #4 (comment).

PR checklist

I have added description of the change I'm proposing in the OpenMS Documentation.
I have read and followed OpenMS Documentation Contributing guidelines.
I have attached a screenshot of the relevant area after this change.
CHANGELOG.md is updated.
I have added my name in CONTRIBUTING.md.

Fixes OpenMS#14.

trickyck · 2022-05-26T07:39:45Z

docs/introduction.md

+
+![](images/introduction/spectrum_peakmap.png)
+
+Left image displays spectrum with peaks (m/z and intensity values) and right image shows spectra stacked in retention


The left image

and the right image

And "a spectrum"

trickyck · 2022-05-26T07:42:14Z

docs/introduction.md

+proteins and metabolites. They employ large-scale experimental techniques that allow acquiring data at the level of
+cellular systems to whole organisms. One of the main analytical method to identify, characterize or quantify proteins
+and metabolites is mass spectrometry (MS) combined with chromatographic separation.
+


Mass spectrometry combined with chromatographic separation is commonly used to identify, characterize or quantify the amount of proteins and metabolites.

trickyck · 2022-05-26T07:43:18Z

docs/introduction.md

+
+# Liquid Chromatography
+
+LC aims to reduce the complexity of the measured sample by separating analytes based on their physicochemical properties.


Liquid Chromatography (LC)
or Liquid chromatography

trickyck · 2022-05-26T07:43:40Z

docs/introduction.md

+to achieve a high degree of separation. In HPLC, peptides are separated on a column. Solved in a pressurized liquid
+(mobile phase) they are pumped through a solid adsorbent material (stationary phase) packet into a capillary column.
+Physicochemical properties of each peptide determine how strongly it interacts with the stationary phase. The most
+commonly HPLC technique in proteomics and metabolomics uses reversed-phase chromatography (RPC) columns. RPC employs a


The most common

The most common HPLC technique in proteomics and metabolomics uses reversed-phase chromatography (RPC) columns.

jpfeuffer

Minor comments

jpfeuffer · 2022-05-26T09:07:14Z

docs/introduction.md

-currently the Eberhard-Karls-Universität in Tübingen, the Freie Universität
-Berlin, and the ETH Zürich.
+```{note}
+Note: This introduction is aimed at users new to the field of LC-MS data analysis and will introduce some basics terms


Will this be fine on sphinx or will it be double Note Note:?

docs/introduction.md

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

@jpfeuffer

* Changed format to backticks for code and bold for tools and UI elements (#33) * made changes to several files * formatted text with backticks and bold * add internal link within the page to quality-control.md * removed backticks from Qt and related software * Fixes: review comments by @greengypsy (#34) * Fixes: review comments by @greengypsy * review fixes and add a few links to tutorials * Added keyboard syntax plus other minor changes (#35) * added keyboard syntax plus other minor changes such as adding full stops to sentences * added spaces between symbols as discussed Co-authored-by: Tapasweni Pathak <tapaswenipathak@gmail.com> * Use correct admonitions (#36) * added one note to installation on gnu linux md file * added one note to installation on gnu linux md file * added admonitions to noted text * changed admonition types as discussed in review * Add downloads page * Add introduction of a few concepts (#39) * Add introduction of a few concepts Fixes #14. * Fixes: review comments by @greengypsy * Fixes: review comments by @jpfeuffer * Update docs/introduction.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * Update docs/introduction.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * Update docs/introduction.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * Update docs/introduction.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * delete: redundant note Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * More docs (#40) * created About.rst * linked Developer FAQ to external website * linked Developer FAQ to external website * linked Developer FAQ to external website * fix links in About.rst * Update About.rst * Update About.rst * Update About.rst * changed About.rst to about.rst * Rename About.rst to about.rst * added known-issues.rst * fix bullet point in known-rst * add code to known-issues.rst * add code to known-issues.rst * fix code to known-issues.rst * added VS output to known-issues.rst * added VS output to known-issues.rst * added VS output to known-issues.rst * added VS output to known-issues.rst * added VS output to known-issues.rst * added more text to known-issues.rst * tried adding console code to known-issues.rst * completed copying content for known-issues.rst * added topp-faq.rst and docutils.conf * changed contents title in topp-faq.rst * inline cpp class in topp-faq.rst * FileInfo is not a cpp class its a tool * adding console code * adding console code * adding console code * add monospace text to topp-faq.rst * fixed code blocks * created about contact for-developers for-users reporting-bugs-issues rst files * created developer-faq.rst * developer-faq changes * developer-faq changes * developer-faq changes * developer-faq changes * testing * developer-faq * developer-faq * developer-faq * developer-faq * developer-faq * developer-faq * developer-faq * minor change * renamed folder to lower case * made small changes to files and created 3 empty .md files * added pyopenmswrapping classes link * removed about.rst and added about.md * added contact.md * created for-developers.md * modified for-developers.md * created building-openms.md * just checking links in contact.md * added contributor quickstart guide, users quick start guide and reporting bugs and issues md files * added linkstobs to flag dead links * fixed some links and deleted for-developers.md * modified about.md, deleted building-openms.md, created build-openms-from-source.md, developer-faq.md * modified quickstart guide contributors, developer faq, reporting bugs, and user quick start guide * added coding convents and write and label github issues md files, edited several others * added Notes to developer-faq.md plus other minor edits * added contributor-faq * added coding-convetions.md * added contributor-faq.md * updated pull request checklist md file * updated write-and-label-github-issues * made changes suggested in the review * updated folder structure as suggested in review * added installations folder with build-openms-from-source.md as discussed * created openms-git-workflow.md and click-fork.png under new directories additional-resources and images * minor changes * fix spacing issues * fix alignment issues * Add a few more from #4 * Fixes: review comments by @jpfeuffer Co-authored-by: greengypsy <ckumar073@gmail.com> Co-authored-by: greengypsy <31978630+greengypsy@users.noreply.github.com> * Add lexers to project (#47) * modified conf.py and requirements.txt to include pygments code * added lexers to code in several files * Add conda installation instructions and a few reorderings (#38) Fixes #15. Fixes #16. * Add wiki and a few more docs (#48) * Add: Adding your own tool to the TOPP suite * Add: writing and shipping external code using openms * Add: Compiling with self built compilers and non default standard libraries * Add: wiki: Build your own OpenMS KNIME package * Add: wiki: OpenMS-2.0-kernel-whitepaper * Add: wiki: Developer Guidelines for adding new dependent libraries * Add: Glossary 🎉 (#49) * Production ready[1]: Touchup and cleanup (#51) * Add: build-openms-from-source in sidebar menu * let's make everything work on staging-openms, too * reduce: sidebar menu under introduction * reduce: sidebar menu list * Add: a few sections in sidebar menu of topp tut * Add tabs for installations using installers Fixes #17. * minor fixes + cleanup * add Discord invite link * Update docs/tutorials/TOPP/quality-control.md Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> * Spell out RC * Production ready[2]: Touchup and cleanup (#58) * fix: follow Sentence case for h2 or less * fix: glossary terms in introduction page * add tabs: ux * fix: follow Title Case and reword * add: description plus file name * fix: dropdown menu sidebar toppas tut * add: +reword .github templates * add: more glossary * fix: include faq * add: glossary more Co-authored-by: greengypsy <31978630+greengypsy@users.noreply.github.com> Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> Co-authored-by: greengypsy <ckumar073@gmail.com>

Add introduction of a few concepts

4347281

Fixes OpenMS#14.

trickyck reviewed May 26, 2022

View reviewed changes

tapaswenipathak requested a review from jpfeuffer May 26, 2022 07:52

tapaswenipathak added 2 commits May 26, 2022 13:30

Fixes: review comments by @greengypsy

2b93915

Fixes: review comments by @jpfeuffer

f179028

jpfeuffer requested changes May 26, 2022

View reviewed changes

tapaswenipathak and others added 5 commits May 26, 2022 17:20

Update docs/introduction.md

7847ba8

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

Update docs/introduction.md

a705f21

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

Update docs/introduction.md

494a329

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

Update docs/introduction.md

3cb2723

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

delete: redundant note

ffadcc8

tapaswenipathak merged commit 5bc8d23 into OpenMS:staging May 26, 2022

tapaswenipathak deleted the issue-14 branch May 26, 2022 12:05

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		![](images/introduction/spectrum_peakmap.png)

		Left image displays spectrum with peaks (m/z and intensity values) and right image shows spectra stacked in retention


		# Liquid Chromatography

		LC aims to reduce the complexity of the measured sample by separating analytes based on their physicochemical properties.

Add introduction of a few concepts #39

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