cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5qv3cd4n
title: MassIVE MSV000091058 - Extracellular Vesicle Contents of Mouse Trophoblast Cells and Their Predicted Influence on Fetal Brain Development
title: The placenta serves as the primary communication organ between mother and fetus. It is essential for gas, nutrient, waste, and hormonal exchange. The precise mechanisms behind how the placenta shapes fetal organ development, however, remain uncertain. The fetal brain is especially dependent upon the placenta for nutrients, hormones, and likely neurotransmitters to guide its early development. The tight linkage between the two organs has given rise to the term, the placenta-brain axis. Serotonin (5-HT) and dopamine may shuttle from the placenta to sculpt early brain formation. The placenta also produces a unique signature pattern of miRNAs. How these factors evade fetal metabolism to reach the developing brain in appreciable concentrations remains uncertain. Extracellular vesicles (EVs) might act a shell to protect their contents and transport these structures to remote target organs, including the brain. Current work characterizes small RNA, proteins, and neurotransmitters within EVs derived from culture media of undifferentiated mouse trophoblast stem cells (mTSC), and mTSC differentiated into pTGCs. Protein and small RNAs differed depending on whether the EVs were derived from pTGC vs. TSC. EVs derived from pTGC vs. TSC contained physiological amounts of 5-HT, dopamine, and norepinephrine that could affect fetal brain development. Small nucleolar (sno)RNAs were upregulated in EVs from pTGC relative to TSC, and these molecules might also affect neuroregulatory genes. Primary target of miRNAs from TSC and pTGC are mRNAs enriched in the fetal brain. Placenta-derived EV might thus hold the key to understanding neurobehavioral disorders that arise from disruptions in the placenta-brain axis.
DOI: 10.25345/c5qz22m9p
title: MassIVE MSV000089636 - Proteomic analysis for immunoprecipitation on TgIST from Toxoplasma infected human U3A or U3A-STAT1 cells
title: This is an experiment designed on exploring human protein complexes interacted with a virulence protein TgIST secreted from Toxoplasma gondii. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed on TgIST IP samples from human cells U3A or U3A-STAT1, treated with IFN-gamma. Served as the Supplementary Data for Fig 1b and Fig 1c.
DOI: 10.25345/c5qz22n0s
title: MassIVE MSV000089844 - Sarikaya_HistoryMyopathy_P124_OrbiElite
title: This dataset consists of 4 raw MS files, acquired on Orbitrap Elite mass spectrometer operated in Data Dependent Acquisition mode. Samples were generated by Ege Sarikaya. Sample processing was performed by Ege Sarikaya and Cassandra Wong. Mass spectrometry acquisition and data analysis was performed by Cassandra Wong. The files are associated with a manuscript submitted for publication by Ege Sarikaya et al. The paper performed a natural history study of Mtm1 KO mice to better understand X-linked myotubular myopathy (XLMTM) disease pathomechanisms. James J. Dowling is the corresponding author of the manuscript (james.dowling@sickkids.ca); Karen Colwill should be contacted for questions on this dataset (colwill@lunenfeld.ca) This submission is associated with 3 Supplementary File (in addition to this README file) Table 1 describes the composition of this dataset Table 2 lists all the peptide evidence (as per iProphet) Table 3 lists the SAINTexpress interactions
DOI: 10.25345/c5qz22n18
title: MassIVE MSV000090021 - GNPS - M. bovis BCG cultured in Glucose vs Oleate MSMS microbeMASST submission
title: Polar Lipidome of M. bovis BCG cultured in 7H9 media without Carbon source, with Glucose or with Oleate. Qualitative LC-MSMS (IDA mode)
DOI: 10.25345/c5qz22n2r
title: MassIVE MSV000090220 - 220827_JH_HowLow_GreenTea_smallDataset
title: Untargeted mass spectrometry metabolomics is an increasingly popular approach for characterizing complex mixtures. Recent studies have highlighted the impact of data pre-processing for determining the quality of metabolomics data analysis. The first step in data processing with untargeted metabolomics requires that signal thresholds be selected for which features (detected ions) are included in the dataset. Analysts face the challenge of knowing where to set these thresholds; setting them too high could mean missing relevant features but setting them too low could result in a complex and unwieldy dataset. This study compared data interpretation for an example metabolomics dataset when intensity thresholds were set at a range of feature heights. The main observations were that low signal thresholds 1) improved limit of detection, 2) in-creased the number of features detected with an associated isotope pattern and/or MS-MS fragmentation spectrum and 3) increased the number of in-source clusters and fragments detected for known analytes of interest. When the series of parameters differing in intensities were applied on a set of 39 samples to discriminate the samples through principal component analyses (PCA), similar results were obtained with both low and high intensity thresholds. We conclude that the most information-rich datasets can be obtained by setting low-intensity thresholds. However, in cases where only a qualitative comparison of samples with PCA is to be performed, it may be sufficient to set high thresholds and thereby re-duce the complexity of the data processing and amount of computational time required.
DOI: 10.25345/c5qz22n37
title: MassIVE Reanalysis RMSV000000668.330 - CCMS ProteoCarta ModDecode reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_6075) [launched by ab1ddc566e8244bd975da925e6cb9107]
title: CCMS ProteoCarta peptidoform interpretation (ModDecode) of Maestro open modification search results for Mus musculus (Cell_line_6075) from MSV000089856/PXD030983.
DOI: 10.6084/m9.figshare.22154531.v1
title: Root trait plasticity.xlsx

description: We separated cleaned root samples into nodal roots and lateral roots according to position. Nodal roots were dried at 65 ℃ for 48 h and weighed. However, for lateral roots that are considered highly plastic, we randomly selected subsamples for scanning, while the remainder was dried as well. Root subsamples were scanned, then also dried and weighed. We then calculated root diameter (mm), specific root length (m g-1), specific surface area (m2 g-1), root tissue density (g m-3) and root length proportions with different diameter by analyzing scanned images using WinRHIZO software (Regent Instruments Inc., Quebec City, QC, Canada). Three parts were classified according to average diameter: fine roots (&lt; 0.2 mm), middle roots (0.2 - 0.8 mm) and thick roots (&gt; 0.8 mm) (Li et al., 2017a). We also calculated root biomass density (g cm-3), root length density (cm cm-3), and biomass allocation to lateral roots (%).
DOI: 10.25345/c5qz22n4q
title: MassIVE MSV000090453 - Sleep prevents brain phosphoproteome disruption to safguard survival
title: Qutantitative proteomic/phosphoproteomic studies of prolonged sleep deprivation mice models.
DOI: 10.25345/c5qz22n56
title: MassIVE MSV000090837 - DIA_staggered_LFQ_Benchmark_High-Performance_QE-HF_30,90,150minGradient
title: LFQ Benchmark with samples from commercial digests according to Kuharev, Joerg, et al. (2015) Sample A: 5% E.coli, 30 % Yeast, 65% Human, 0.9ug on column Sample B: 20% E.coli, 15% Yeast, 65% Human, 0.9ug on column (4 replicates per gradient length, one aliquot per 4 samples from one mastermix per sample type) Expected log2 fold-changes of -2,0,+1 for E.coli, Human, Yeast. Sample C: 0.9ug on column, average of A and B used to build enhanced spectral library by Gas-Phase-Fractionation. Sample C files are here for completeness, obtained libraries can lead to improvements by I do not use refined libraries for my applications anymore, use at own caution and risk. Notably, the chromatography was performed with uPAC analytical column, resulting in sharp and symmetric &lt;20s short chromatograms. Gradients (30,90,150 min) were 2-sloped and linear, with the last third of the gradient encompassing half of the %B increase. Analysis with Spectronaut might not be ideal as MS1 was recorded at 30k resolution. This dataset, in particular the 90min gradient ones, can possibly lead to the strongest LFQ benchmark results and might serve as upper standards in comparisons.
DOI: 10.25345/c5qz22n6p
title: MassIVE Reanalysis RMSV000000354.6144 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SYNPR [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22n75
title: MassIVE Reanalysis RMSV000000354.6350 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TRDMT1 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22n8n
title: MassIVE Reanalysis RMSV000000354.6528 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DNAJB11 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22n94
title: MassIVE Reanalysis RMSV000000354.6736 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C6orf127 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p07
title: MassIVE Reanalysis RMSV000000354.7122 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GSG1 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p1q
title: MassIVE Reanalysis RMSV000000354.7507 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, LRRN2 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p26
title: MassIVE Reanalysis RMSV000000354.7894 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CYB5A [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p3p
title: MassIVE Reanalysis RMSV000000354.8103 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RAB32 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p45
title: MassIVE Reanalysis RMSV000000354.8280 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, AIMP1 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p5n
title: MassIVE Reanalysis RMSV000000354.8489 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NDUFS1 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p64
title: MassIVE Reanalysis RMSV000000354.8875 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TSEN2 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p7m
title: MassIVE Reanalysis RMSV000000354.9268 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C9orf116 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p83
title: MassIVE Reanalysis RMSV000000354.9649 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, INTS4 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22p9k
title: MassIVE Reanalysis RMSV000000354.10036 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ANKRD49 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22q0p
title: MassIVE Reanalysis RMSV000000354.10244 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TYW3 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22q15
title: MassIVE Reanalysis RMSV000000354.10421 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GJB4 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22q2n
title: MassIVE Reanalysis RMSV000000354.10633 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, UBXN11 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22q34
title: MassIVE Reanalysis RMSV000000354.11017 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, WDR85 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5qz22q4m
title: MassIVE MSV000090960 - Invitro_PKS14-overecpressing and PKS14-knockout strain
title: PKS14-overecpressing and PKS14-knockout strain were inoculated into PDB for 7 days. The fungal cells were extracted with methanol, and the culture broth was extracted with ethyl acetate.
DOI: 10.25345/c5qz22q53
title: MassIVE Reanalysis RMSV000000355.4514 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, API5 [launched by dab8bba1f45f4e4082f7fa74fbbf30fb]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.