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GNPS - Incorporating in-source fragment information improves metabolite identification accuracy in untargeted LC-MS datasets

ABSTRACT: This is a reanalysis of the data collected as a part of the MTBLS67 and MTBLS297 studies, associated with the manuscript "Incorporating in-source fragment information improves metabolite identification accuracy in untargeted LC-MS datasets" Included are the original raw files with all MS/MS scans removed, as well as Scaffold Elements results files (in the supplementary information) The MS/MS scans were removed using Proteowizard MSConvertGUI 3.0.9987

INSTRUMENT(S): LTQ Orbitrap, TripleTOF 5600

ORGANISM(S): Solanum Lycopersicum (ncbitaxon:4081) Schizosaccharomyces Pombe (ncbitaxon:4896)

SUBMITTER: Phillip Seitzer

PROVIDER: MSV000082986 | GNPS |

REPOSITORIES: GNPS

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Incorporating in-source fragment information improves metabolite identification accuracy in untargeted LC-MS datasets

Project description:This is a reanalysis of the data collected as a part of the MTBLS67 and MTBLS297 studies, associated with the manuscript "Incorporating in-source fragment information improves metabolite identification accuracy in untargeted LC-MS datasets" Included are the original raw files with all MS/MS scans removed, as well as Scaffold Elements results files (in the supplementary information) The MS/MS scans were removed using Proteowizard MSConvertGUI 3.0.9987

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Project description:Amniotic fluid (AF) is a complex biological material that provides a unique window into the developing human. Residual AF supernatant contains cell-free fetal RNA. The objective of this study was to develop an understanding of the AF core transcriptome by identifying the transcripts ubiquitously present in the AF supernatant of euploid midtrimester fetuses. We detected 476 well-annotated genes present in all twelve AF samples. Functional analysis identified 6 physiological systems represented in the AF core transcriptome, including musculoskeletal and nervous system development and function and embryonic/ organismal development. mTOR signaling was identified as a key canonical pathway. Twenty-three highly organ-specific transcripts were identified; six of these are known to be highly expressed by fetal brain. This study demonstrates that AF cell-free fetal RNA can provide biological information about multiple fetal organ systems. This was an in silico investigation of gene expression in 12 euploid midtrimester AF samples acquired primarily for advanced maternal age. We focused on the transcripts called M-bM-^@M-^\presentM-bM-^@M-^] in all of the samples. Functional analyses were performed using Ingenuity software. Fetal-organ specificity was examined for each transcript using the GNF Gene Expression Atlas. For fetal organs not represented in the atlas, manual literature searching and Ingenuity analysis were used.

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