Informed-Proteomics: open-source software package for top-down proteomics.
Jungkap ParkPaul D PiehowskiChristopher WilkinsMowei ZhouJoshua MendozaGrant M FujimotoBryson C GibbonsJared B ShawYufeng ShenAnil K ShuklaRonald J MooreTao LiuVladislav A PetyukNikola TolićLjiljana Paša-TolićRichard D SmithSamuel H PayneSangtae KimPublished in: Nature methods (2017)
Top-down proteomics, the analysis of intact proteins in their endogenous form, preserves valuable information about post-translation modifications, isoforms and proteolytic processing. The quality of top-down liquid chromatography-tandem MS (LC-MS/MS) data sets is rapidly increasing on account of advances in instrumentation and sample-processing protocols. However, top-down mass spectra are substantially more complex than conventional bottom-up data. New algorithms and software tools for confident proteoform identification and quantification are needed. Here we present Informed-Proteomics, an open-source software suite for top-down proteomics analysis that consists of an LC-MS feature-finding algorithm, a database search algorithm, and an interactive results viewer. We compare our tool with several other popular tools using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.
Keyphrases
- mass spectrometry
- liquid chromatography
- machine learning
- label free
- deep learning
- data analysis
- endothelial cells
- electronic health record
- big data
- high resolution mass spectrometry
- gas chromatography
- high resolution
- emergency department
- healthcare
- artificial intelligence
- tandem mass spectrometry
- simultaneous determination
- wastewater treatment
- induced pluripotent stem cells
- molecular dynamics
- neural network
- health information
- adverse drug
- density functional theory
- solid phase extraction