Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats

[Johan T. <joh...@im...>]

Hi Jenny,

Having access to a binary format could clearly benefit many applications. Will this format be solely intended for ion mobility experiments, or do you also aim to target "regular" experiment data?

The HDF5 library was utilized once already for a MS data format: mz5 (http://www.mcponline.org/content/11/1/O111.011379.full.pdf+html), maybe something can be reused from there. Depending on how data will be stored locally, numerical compression through Numpress might be interesting? Further I would recommend to walk the extra mile and benchmark the file format using data-files from different vendors and on different samples. Your result will vary depending on data density.

A last mention is that I've had great experience with Google protobuf based binary file format, if the HDF5 does not work out for you. Protobuf does NOT have any support for random access though, so that would require a custom solution.

Just my few cents, good luck with the implementation!

/J

Johan Teleman
Ph.D. student
Dept. of Immunotechnology
Lund University

________________________________________
Från: jeleclai [jel...@un...]
Skickat: den 25 januari 2016 13:34
Till: psi...@li...
Kopia: Navarro, Pedro
Ämne: [Psidev-ms-dev] HDF5-based mass spectrometry formats

Hi all,

I am a Phd student in Stefan Tenzer's lab. We are currently working on a
new format for mass spectrometric data, based on HDF5.

We started to develop this format because we struggled with ion mobility
data: random access data to vendor's raw files is, as everyone knows,
suboptimal, and especially in the case of including ion mobility, we
foresee better ways to organize MS data in order to improve random access.

In this regard, the HDF5 library is of great advantage as it combines a
simple and flexible way to structure the data with several efficient
methods for I/O access.

Additionally, HDF5 library offers a good support for developers. It is
already successfully implemented in many other scientific fields like
Astronomy, Climatology, Genetics... All of this makes it a good
candidate for future developing of standard formats of large data, which
are interrogated in a random access way.

We would be very happy to bring this topic to discussion for the next
PSI meeting!

Best wishes,

Jenny

--

Jennifer Leclaire
M.Sc. Angewandte Bioinformatik

--------------------------------------------------
Institut für Immunologie
Universitätsmedizin der
Johannes Gutenberg-Universität
Langenbeckstr.1
55131 Mainz
www.immunologie.uni-mainz.de


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