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PXD027359

PXD027359 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAlphaTims: Indexing unprocessed trapped ion mobility spectrometry - time of flight data for fast and easy accession and visualization
DescriptionHigh resolution mass spectrometry-based proteomics generates large amounts of data, even in the standard liquid chromatography (LC) – tandem mass spectrometry configuration. Adding an ion mobility dimension vastly increases the acquired data volume, challenging both analytical processing pipelines and especially data exploration by scientists. This has necessitated data aggregation, effectively discarding much of the information present in these rich data sets. Taking trapped ion mobility spectrometry (TIMS) on the quadrupole time of flight platform (Q-TOF) as an example, we developed an efficient indexing scheme that represents all data points as detector arrival times on scales of seconds (LC), milliseconds (TIMS) and microseconds (TOF). In our open source AlphaTims package, data are indexed, accessed and visualized by a combination of tools of the scientific Python ecosystem. We interpret unprocessed data as a sparse 4D matrix and use just in time compilation to machine code with Numba, accelerating our computational procedures by several orders of magnitude while keeping to familiar indexing and slicing notations. For samples with more than six billion detector events a modern laptop can load and index raw data in about a minute. Loading is even faster when AlphaTims has already saved indexed data in a HDF5 file, a portable scientific standard used in extremely large-scale data acquisition. Subsequently, data accession along any dimension and interactive visualization happen in milliseconds. We have found AlphaTims to be a key enabling tool to explore high dimensional LC-TIMS-Q-TOF data and have made it freely available as an open-source Python package with a stand-alone graphical user interface at https://github.com/MannLabs/alphatims or as part of the AlphaPept framework.
HostingRepositoryPRIDE
AnnounceDate2021-07-30
AnnouncementXMLSubmission_2021-07-30_00:06:56.377.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMario Oroshi
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumenttimsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-07-16 03:54:48ID requested
12021-07-30 00:06:56announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Mass spectrometry, ion mobility spectrometry, time of flight, data indexing, data visualization, software.
Contact List
Matthias Mann
contact affiliationDepartment of Proteomics and Signal Transduction Max Planck Institute of Biochemistry
contact emailmmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliationProteomics
contact emailoroshi@biochem.mpg.de
dataset submitter
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Dataset FTP location
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PRIDE project URI
Repository Record List
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