160 Citations
Aird: A computation-oriented mass spectrometry data format enables higher compression ratio and less decoding time
- Computer SciencebioRxiv
- 2020
Aird is described, an opensource and computation-oriented format with controllable precision, flexible indexing strategies and high compression rate, which uses JavaScript Object Notation for metadata storage, multiple indexing, and reordered storage strategies for higher speed of data randomly reading.
Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects.
- BiologyThe annals of applied statistics
- 2010
An overview of bottom-up proteomics is presented and the key statistical issues that arise in protein identification and quantification are outlined, as well as the application of sound statistical principles for estimation and inference.
Molecular mass spectrometry imaging in biomedical and life science research
- ChemistryHistochemistry and Cell Biology
- 2010
This review describes the current state of mass spectrometry imaging (MSI) in life sciences and offers a thorough introduction to the MSI workflows, principles and areas of application.
Bioinformatics in Lipidomics: Automating Large-Scale LC-MS-Based Untargeted Lipidomics Profiling with SimLipid Software.
- BiologyMethods in molecular biology
- 2022
SimLipid software is presented, which contains a customizable library of lipid species; graphical user interfaces for visualization of raw data; the identified lipid molecules and their associated mass spectra annotated with fragment ions and parent ions; and detailed information of each identified lipid species all in a single workbench enabling users to rapidly review the results.
HMDB 5.0: the Human Metabolome Database for 2022
- ChemistryNucleic acids research
- 2022
These upgrades and updates should greatly enhance the HMDB’s ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.
StackZDPD: a novel encoding scheme for mass spectrometry data optimized for speed and compression ratio
- Computer ScienceScientific reports
- 2022
Stack-ZDPD reduces the volume of data stored in mzML format by around 80% or more, depending on the data acquisition pattern, and the compression ratio is approximately 30% compared to ZDPD for data generated using Time of Flight technology.
Software Options for the Analysis of MS-Proteomic Data.
- BiologyMethods in molecular biology
- 2021
This chapter illustrates the most popular bioinformatics solution for the analysis of shotgun MS-proteomics data, which consists in the enzymatic digestion of protein into peptides that are then measured by MS-instruments through a data dependent acquisition (DDA) mode.
References
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The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world
- Computer ScienceBriefings Bioinform.
- 2008
The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was tasked with the creation of data standards and interchange formats to allow both the exchange and storage of such data irrespective of the hardware and software from which it was generated.
A common open representation of mass spectrometry data and its application to proteomics research
- BiologyNature Biotechnology
- 2004
The 'mzXML' format is introduced, an open, generic XML (extensible markup language) representation of MS data that will facilitate data management, interpretation and dissemination in proteomics research.
Corrigendum: Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors
- BiologyNature Biotechnology
- 2004
In the author list, the name of author Seong-il Lee was misspelled as Sung-Il Lee.