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smith-chem-wisc / FlashLFQ

Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics
GNU Lesser General Public License v3.0
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numpress? #70

Open jvolkening opened 6 years ago

jvolkening commented 6 years ago

Hello all. I was getting the rather vague error 

Problem opening mzml file spectra/Ctrl1_5min_total.mzML; One or more errors occurred.

When I re-converted my files using different settings, I was able to get things to work.

Am I right in thinking that mzLib (and thus FlashLFQ) does not support Numpress compression in mzML?

acesnik commented 6 years ago

We could use this Numpress implementation. https://github.com/topdownproteomics/sdk/tree/master/src/TopDownProteomics/Tools

acesnik commented 6 years ago

But currently, I don't believe we support Numpress compression.

trishorts commented 6 years ago

Mol Cell Proteomics. 2014 Jun; 13(6): 1537–1542. Published online 2014 Mar 27. doi: 10.1074/mcp.O114.037879 PMCID: PMC4047472 PMID: 24677029 Numerical Compression Schemes for Proteomics Mass Spectrometry Data* Johan Teleman,‡ Andrew W. Dowsey,§¶ Faviel F. Gonzalez-Galarza,‖ Simon Perkins,‖ Brian Pratt,** Hannes L. Röst,‡‡ Lars Malmström,‡‡ Johan Malmström,§§ Andrew R. Jones,‖ Eric W. Deutsch,¶¶,a,b and Fredrik Levander‡‖‖,b Author information ► Article notes ► Copyright and License information ► Disclaimer This article has been cited by other articles in PMC. Go to: Abstract The open XML format mzML, used for representation of MS data, is pivotal for the development of platform-independent MS analysis software. Although conversion from vendor formats to mzML must take place on a platform on which the vendor libraries are available (i.e. Windows), once mzML files have been generated, they can be used on any platform. However, the mzML format has turned out to be less efficient than vendor formats. In many cases, the naïve mzML representation is fourfold or even up to 18-fold larger compared with the original vendor file. In disk I/O limited setups, a larger data file also leads to longer processing times, which is a problem given the data production rates of modern mass spectrometers. In an attempt to reduce this problem, we here present a family of numerical compression algorithms called MS-Numpress, intended for efficient compression of MS data. To facilitate ease of adoption, the algorithms target the binary data in the mzML standard, and support in main proteomics tools is already available. Using a test set of 10 representative MS data files we demonstrate typical file size decreases of 90% when combined with traditional compression, as well as read time decreases of up to 50%. It is envisaged that these improvements will be beneficial for data handling within the MS community.