Talk:List of mass spectrometry software

Proposed Re-organisation
Coming fresh to this page it seems to have a strange order. Proteo and meta omics are specialised and it would make far more sense to start with basic mass spectrometry before looking at software for GC-MS and basic LC-MS before moving onto the more complex subjects and then within the individual sections it should be done in alphabetical order Chppjs  —Preceding undated comment added 22:14, 15 February 2020 (UTC)

Proposed merge
From SEQUEST and MzXML. --Kkmurray 18:35, 20 April 2007 (UTC)
 * I removed the merge flag (see Wikipedia_talk:WikiProject_Mass_spectrometry). The article should probably be reworked to fit into Category:Lists of software. --Kkmurray 18:35, 20 April 2007 (UTC)

MudpIT query
I am quoting a part from the article "... tandem mass spectrometry (also known as MS/MS or MS2) experiments (sometimes called shotgun proteomics or MuDPiT (Multidimensional Protein Identification Technology) experiments) are ..."- I highly doubt that MS?MS is called MudPIT. They are used in different contexts i believe. Please confirm and correct it if possible. —Preceding unsigned comment added by Amityadavigib (talk • contribs) 19:27, 13 October 2009 (UTC)

Sub-Group Organization

 * Do others object to (me or anyone else) re-organizing the list of software into alphabetical order?

I think the separation into mass spec functions are useful, so keeping sequest and mascot in with database searching, denovoS and lutefisk in with de novo, and so forth is fine. My suggestion is to alplhabetize within each of these sub-groups.


 * Also, does anyone care to make suggestions for other categories we could include...rather than just a catch all "other" field? I'm not trying to make the page unncessarily long, just organized.

DavidTrin (talk) 18:11, 22 December 2009 (UTC)


 * It should really be in paragraph form per WP:NOTDIRECTORY --Kkmurray (talk) 19:57, 28 December 2009 (UTC)


 * A lot of the other software lists (see talk above) are fairly list-like, though with some comment between them. As for categories Open Source/Proprietary can be a useful split - anyone object if I introduce this? --Y_Less&#124; &#8516;&#8254;&#741;&#477;ss  14:02, 11 July 2011 (UTC)

Move
I moved the page to the singular 'software' per MOS:RETAIN and consistency within Category:Lists_of_software. --Kkmurray (talk) 14:22, 15 May 2014 (UTC)

External links modified
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 * Added archive https://web.archive.org/20150416062601/http://www.massmatrix.net:80/mm-cgi/home.py to http://www.massmatrix.net/mm-cgi/home.py
 * Added archive https://web.archive.org/20101024191936/http://masswiz.igib.res.in:80/ to http://masswiz.igib.res.in/
 * Added archive https://web.archive.org/20130822072658/http://fenchurch.mc.vanderbilt.edu:80/software.php to http://fenchurch.mc.vanderbilt.edu/software.php
 * Added archive https://web.archive.org/20141114121359/http://www.maxquant.org:80/downloads.htm to http://www.maxquant.org/downloads.htm
 * Added archive https://web.archive.org/20110725074514/http://www.bioprocess.org/esiprot/ to http://www.bioprocess.org/esiprot/
 * Added archive https://web.archive.org/20131113153934/http://www.bioprocess.org/esiprot/esiprot_form.php to http://www.bioprocess.org/esiprot/esiprot_form.php
 * Added archive https://web.archive.org/20070902033915/http://massxpert.org/userman/pdf/massxpert.pdf to http://massxpert.org/userman/pdf/massxpert.pdf
 * Added archive https://web.archive.org/20120407022527/http://www.bioproximity.com/content/utility-converting-mass-spectrometry-file to http://www.bioproximity.com/content/utility-converting-mass-spectrometry-file

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External links modified
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Request to add software
Dear Wikipedia editors.

Please consider adding to the liss new software entry:

Section: Other software

Software name: mzAccess

Type of license: open source

Description: Open source web-service software for remote interactive access to the large collections of mass spectrometry data. mzAccess Web API provides ability to call for pieces (like chromatograms or spectra) of raw mass spectrometry data located at web-site

Reference: PMID: 28514166

Link:

website - http://mzaccess.org

github - https://github.com/Yaroslav-Lyutvinskiy

I can't do it by myself as I am author of that software and it is in contradiction with conflict interest rules. Nevertheless, I think this software adds a bit of unique functionality to mass spectrometry software toolset. By the nature it is open source web-service (web-site with API) providing interface to raw mass spectrometry data.

With respect, Yaroslav Lyutvinskiy (talk) 13:52, 15 November 2017 (UTC)

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Only MS/MS?
The article seems to present MS/MS as the only method for protein identification. The article should include the Peptide Mass Fingerprinting strategy which is based on MS analysis. PMF was the first strategy we had for peptide identification and has been used for several decades until today. Protein Prospector and MASCOT have been reference tools for PMF database search from the mid-late 1990's and still used for this purpose. More recent software is dedicated to shotgun MS/MS identification and I am not sure they are capable of PMF identification. The table should include the specific capabilities in this respect. 83.46.2.234 (talk) 14:49, 18 April 2024 (UTC)