[PRE REVIEW]: MZsearch: A Python-Based Compound Identification Tool for GC-MS and LC-MS-Based Metabolomics

[editorialbot]

Submitting author: @hdlugas (Hunter Dlugas)
Repository: https://github.com/hdlugas/MZsearch
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @jromanowska
Reviewers: @joewandy, @aboffin
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/2eb52eca6a3059e70d545a302e54efce/status.svg)](https://joss.theoj.org/papers/2eb52eca6a3059e70d545a302e54efce)

Author instructions

Thanks for submitting your paper to JOSS @hdlugas. Currently, there isn't a JOSS editor assigned to your paper.

@hdlugas if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.32 s (69.6 files/s, 644394.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              4              0              0         200212
Python                           8            388            233           1057
Bourne Shell                     5            141              0            733
Markdown                         2            123              0            568
TeX                              1             16              0            182
YAML                             2              1              4             30
-------------------------------------------------------------------------------
SUM:                            22            669            237         202782
-------------------------------------------------------------------------------

Commit count by author:

   209	hdlugas

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1979

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/joss.02411 is OK
- 10.1016/1044-0305(94)87009-8 is OK
- 10.1038/s41592-021-01331-z is OK
- 10.1093/bioinformatics/btab583 is OK
- 10.1002/pmic.201300246 is OK
- 10.1038/nmeth.3959 is OK
- 10.1021/acs.analchem.9b04884 is OK
- 10.1093/bioinformatics/btab583 is OK
- 10.1016/j.chemolab.2023.104861 is OK
- 10.26434/chemrxiv-2024-5fm7t is OK
- 10.5281/zenodo.12786324 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Quantification method of classification processes....

❌ MISSING DOIs

- 10.1007/bf01016429 may be a valid DOI for title: Possible generalization of Boltzmann-Gibbs statist...
- 10.1093/bioinformatics/bts083 may be a valid DOI for title: A method of finding optimal weight factors for com...
- 10.2139/ssrn.4375943 may be a valid DOI for title: ShinyMetID: An R shiny package for metabolite iden...

❌ INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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subMALDI: an open framework R package for processing irregularly-spaced mass spectrometry data
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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@hdlugas thanks for your submission to JOSS. To help check if this work is in scope for JOSS, I've just flagged it for scope review by our editorial board. This is because of the relatively small size of the project. Among other things, the scope check will determine if the project conforms to our substantial scholarly effort criterion.
The scope review should take about 2 weeks to complete.

[Kevin-Mattheus-Moerman]

@hdlugas just a small update. It looks like we need a bit longer to check the scope for this submission. I hope to be able to get back to you with a verdict within a week. Thanks for your patience.

[Kevin-Mattheus-Moerman]

@hdlugas the scope review has determined this work may be in scope for JOSS. I'll now look for a handling editor.

[Kevin-Mattheus-Moerman]

@editorialbot invite @lpantano as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@lpantano do you think you can edit this one, or the other paper I invited you for?

[Kevin-Mattheus-Moerman]

@hdlugas as we are processing a large backlog of submission, unfortunately all editors in this domain are busy handling other submissions. I have just invited one but they may not be available either. Hence I have just waitlisted this submission. We will assign an editor as soon as one becomes available.

[hdlugas]

@Kevin-Mattheus-Moerman sounds good, thanks for letting us know.

[Kevin-Mattheus-Moerman]

@editorialbot invite @jromanowska as editor

[editorialbot]

Invitation to edit this submission sent!

[jromanowska]

I can take it! However, I'm on sick leave this week - if it's OK, I'll let you know when I'm back to work next week.

[Kevin-Mattheus-Moerman]

@jromanowska okay. Hope you'll feel better soon. I'll assign it now and you can pick it up once you are feeling better.

[Kevin-Mattheus-Moerman]

@editorialbot assign @jromanowska as editor

[editorialbot]

Assigned! @jromanowska is now the editor

[jromanowska]

Hi, @hdlugas 👋
I will take care of the process from now on. I will try to find reviewers, but please let me know if you have any suggestions (or oppositions). When naming reviewers, write their GitHub handles without @, so that they won't get notified.

When it comes to the paper, please reduce the word-count. to around 1000. One thing you can do is to remove the very long command examples - these don't really suit in JOSS paper, but rather in the documentation.
The last thing is to check the DOIs - as noted by editorialbot above, there are some references that have missing DOIs.

[jromanowska]

👋 @joewandy & @hechth, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[joewandy]

Hello there. Thanks for contacting me. I'd be happy to review this submission!

[jromanowska]

Thank you, @joewandy, for quick reply and agreeing to review! Once I find second reviewer, we will start the official review in a new thread. In the meantime, you can take a look at the repo or just wait :)

[jromanowska]

@editorialbot assign @joewandy as reviewer

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[jromanowska]

@editorialbot add @joewandy as reviewer

[editorialbot]

@joewandy added to the reviewers list!

[hdlugas]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

Five most similar historical JOSS papers:

MSMetaEnhancer: A Python package for mass spectra metadata annotation
Submitting author: @hechth
Handling editor: @csoneson (Active)
Reviewers: @marshallmcdonnell, @chryswoods
Similarity score: 0.6982

subMALDI: an open framework R package for processing irregularly-spaced mass spectrometry data
Submitting author: @wesleyburr
Handling editor: @pibion (Retired)
Reviewers: @jspaezp, @sigven, @tystan
Similarity score: 0.6741

ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics
Submitting author: @joewandy
Handling editor: @csoneson (Active)
Reviewers: @jspaezp, @MKoesters
Similarity score: 0.6720

RIAssigner: A package for gas chromatographic retention index calculation
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Similarity score: 0.6659

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Reviewers: @mdhaber, @kostiantyn-kucher
Similarity score: 0.6533

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[jromanowska]

@hdlugas , I'm having hard time finding reviewers - please suggest some names here.

[hdlugas]

@jromanowska Yep, we think the following may have a background suitable for reviewers of our software (GitHub usernames are in parentheses):

• Jianhui Gong (duncanjunegong)
• Lorenzo Castellino (Kastakin)
• Senthil Murugapiran (aboffin)
• adafede (adafede)
• askerdb (askerdb)
• florian-huber (florian-huber).

Lorenzo Castellino and Senthil Murugapiran may be particularly well-suited to review since (i) our software is a Python-based tool to be used in the Bash shell and (ii) these two potential reviewers are familiar with Bash.

Note that we selected possible reviewers as those with an area of expertise in "Biomedical Engineering, Biosciences, Chemistry, and Materials" with Python experience and keyword "metabolomics".

[jromanowska]

👋 @Kastakin & @aboffin, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[aboffin]

@jromanowska Thank you for the opportunity. I will be happy to review, unfortunately I will be able to complete my review only by Jan 10. Let me know if that works.

[Kastakin]

@jromanowska thanks for the consideration. Unfortunately I am in the midst of writing my PhD Thesis and switching careers so I would not be able to give to the review the attention it deserves.
Best of luck to the authors for a work that looks very promising!

[jromanowska]

@aboffin - I think many of us will be away during the holiday season, so I think this is OK. I will start the review and we'll see how it goes :)

[jromanowska]

@Kastakin - thanks for the quick reply! Good luck to you!

[jromanowska]

@editorialbot add @aboffin as reviewer

[editorialbot]

@aboffin added to the reviewers list!

[jromanowska]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7594.