cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5jd4pz99
title: MassIVE MSV000091013 - Transcriptomics and proteomics approach for the identification of altered blood microRNAs and plasma proteins in Parkinson's disease.
title: Parkinson's disease (PD) is a neurodegenerative disorder caused by the selective destruction of dopaminergic neurons (DA-nergic). Clinically, PD is diagnosed based on developing signs and symptoms. A neurological and physical examination and sometime medical and family history also helps in diagnosis of PD. However, most of these features are visible when more than 80% of the dopaminergic neurons are degenerated. The understanding of the selective degeneration process at cellular and molecular level and development of new biomarkers is required for effective PD management. In present study, we have carried out global protein profiling through LC MS/MS and miRNA profiling by using brain-specific miRNA array panel of 112 miRNAs in PD patients and healthy controls to find the unprejudiced group of proteins and miRNAs that are deregulating in PD. Proteomics sample processing: Albumin of the plasma was depleted using PierceTM Albumin Depletion Kit as described by the manufacturer and plasma samples were cleaned by PierceTM Detergent Removal Spin Columns. Protein was quantified by PierceTM bicinchoninic acid (BCA) protein assay kit (Cat# 23227) of Thermo Fisher. 100 microgram of quantified plasma protein from each sample were mixed with 0.1% (V/V) RapiGest SF surfactant and 5mM dithiothreitol (DTT) mixed and incubate at 60 degree Centigrade for 30 min for reduction. Samples were further mixed with 15mM Iodoacetamide (IAA) and incubated the samples in dark for 30 min. (RT) for alkylation of proteins. The proteins were then digested overnight with the enzyme Trypsin/LysC (Cat# V5071) in a 1:30 enzyme/protein ratio at 37degree Centigrade in the water bath. The digest was briefly vortexed and centrifuged at 20000g for 10 min/4 degree Centigrade. The supernatant containing tryptic peptides were collected and further, tryptic peptides were purified and concentrated by passing through Pierce C18 Spin Columns (Cat# 89870). The final tryptic peptides from C18 columns were lyophilized using a lyophilizer. Finally, the lyophilized samples were dissolved in 0.1% FA in water for loading on LC-MS/MS. Data analysis: Proteome Discoverer software (Proteome Discoverer 2.4, Thermo Fisher Scientific) was used to analyze the raw proteomics data from all the samples and the peptide lists were searched against the online Homo sapiens (SwissProtTaxID 9606) Uniprot database with N-terminal acetylation12 and methionine oxidation static modification while cysteine carbamidomethylation as fixed modification. The precursor mass tolerance 10ppm and fragment mass tolerance 0.1Da was set for the database search and maximum two missed cleavage sites were allowed. A 1% FDR (false discovery rate) was used for peptide identification.
DOI: 10.25345/c5jd4q00t
title: MassIVE MSV000091217 - Paullinia_cupana_massive_dataset_JosielAmazonas
title: The guarana extracts were submitted to liquid chromatography analysis coupled with mass spectrometry at the Analytical Center of the Thematic Laboratory of Chemistry of Natural Products-CALTQPN at INPA-Brazil. The extract samples obtained were prepared by weighing them in Eppendorf tubes and solubilizing them in a mixture of MeOH (0.1% formic acid) and 0.1% formic acid solution, in a 1:1 ratio, having the final concentration of 1 mg/mL. Finally, the tubes were centrifuged and transferred to vials for further analysis. The equipment used was a Liquid Chromatograph (Shimadzu, Japan) coupled to a high-resolution Time-of-flight mass spectrometer (MicroTOF QII model, Bruker Daltonics, Bremen, Germany), with an ESI-type ionization source in negative mode. For analysis, a Luna 5u PFP2 100A column (15 cm x 2.00 mm) was used and the mobile phases with the solvents: A: 0.1% formic acid solution. MS/MS parameters: capillary: 3500 volts; Scan: 120-1200m/z; Set nebulizer: 2Bar psi; Set dry Heater: 180 Celsius; Set dry gas: 9.0 L/ min.; Rolling Averages: 1cts.
DOI: 10.25345/c5jh3d63w
title: MassIVE MSV000089799 - Endophytic Fungus Pure Culture (Costa Rica)
title: extract of pure culture broth, first collection (PI: Giselle Tamayo-Castillo, Priscila Chaverri, Ph.D. candidate Efrain Escudero)
DOI: 10.25345/c5jh3d64c
title: MassIVE MSV000090185 - Characterization of sow milk N-liked glycoproteome over the course of lactation
title: Milk is essential for healthy growth and development of infants, with proteins in milk serving as key nutrients and regulators of these processes. Protein activity is affected by modifications made to their structure including the addition of sugar groups called glycans. Here we present the characterization of sow milk proteins with glycan groups on asparagine and glutamine amino acids in colostrum, transitional and mature milk of pigs. We found 220 high confidence (found in two sows on one day) glycoproteins, and that the abundance of glycosylated proteins varied by stage of milk production and number of glycan groups.
DOI: 10.25345/c5jh3d65v
title: MassIVE Reanalysis RMSV000000668.118 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_F1648ZL2) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Cell_line_F1648ZL2) (MSV000089856/PXD030983).
DOI: 10.25345/c5jh3d66b
title: MassIVE Reanalysis RMSV000000668.292 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Thyroid_phosphoproteome) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Male_Thyroid_phosphoproteome) (MSV000089856/PXD030983).
DOI: 10.25345/c5jh3d67t
title: MassIVE Reanalysis RMSV000000666.46 - CCMS ProteoCarta Maestro reanalysis of Zea mays from Growth heterosis in maize is associated with expression heterosis of chloroplast ribosomes (Mixture RIL_RIL317-BioRep34) [launched by 25d00eb062cf42859106267f298c2eec]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Zea mays (Mixture RIL_RIL317-BioRep34) from MSV000085916.
DOI: 10.25345/c5jh3d689
title: MassIVE MSV000090409 - GNPS - MTBLS874: Marine Biodiscovery Ireland 2017 Samples / BDV10017 Alentia gelatinosa
title: The outcomes of this project are to identify bioactive marine natural products from Irish marine life. This specific dataset contains LC-MS/MS spectra from tissue of the marine worm Alentia gelatinosa. Files are part of the Metabolights dataset MTBLS874.
DOI: 10.25345/c5jh3d69s
title: MassIVE MSV000090615 - Root and leaf metabolome of non-mycorrhizal and mycorrhizal seedlings by UHPLC-Orbitrap-MS/MS
title: This study compared mycorrhizal-associated metabolome alterations across multiple plant-mycorrhizal fungus combinations. Specifically, we inoculated a phylogenetically diverse set of temperate tree species with either arbuscular mycorrhizal or ectomycorrhizal fungi (the two major mycorrhizal lifestyles). Using comprehensive metabolomics approaches, we then assessed the metabolome in mycorrhizal and non-mycorrhizal roots and the corresponding leaves.
DOI: 10.25345/c5jh3d70w
title: MassIVE Reanalysis RMSV000000354.5922 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TOB1 [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/c5jh3d71c
title: MassIVE Reanalysis RMSV000000354.6305 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, STIM2 [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/c5jh3d72v
title: MassIVE Reanalysis RMSV000000354.6691 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DDRGK1 [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/c5jh3d73b
title: MassIVE Reanalysis RMSV000000354.6897 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C2orf48 [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/c5jh3d74t
title: MassIVE Reanalysis RMSV000000354.7077 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GLB1 [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/c5jh3d759
title: MassIVE Reanalysis RMSV000000354.7283 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZYX [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/c5jh3d76s
title: MassIVE Reanalysis RMSV000000354.7671 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TXNDC3 [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/c5jh3d778
title: MassIVE Reanalysis RMSV000000354.8058 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SORD [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/c5jh3d78r
title: MassIVE Reanalysis RMSV000000354.8443 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, P2RX5 [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/c5jh3d797
title: MassIVE Reanalysis RMSV000000354.8831 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TUBB [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/c5jh3d80b
title: MassIVE Reanalysis RMSV000000354.9040 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C17orf53 [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/c5jh3d81t
title: MassIVE Reanalysis RMSV000000354.9223 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SEC22B [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/c5jh3d829
title: MassIVE Reanalysis RMSV000000354.9432 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, AHCY [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/c5jh3d83s
title: MassIVE Reanalysis RMSV000000354.9814 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TRMT2A [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/c5jh3d848
title: MassIVE Reanalysis RMSV000000354.10198 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TXNDC11 [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/c5jh3d85r
title: MassIVE Reanalysis RMSV000000354.10588 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, STX5 [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/c5jh3d867
title: MassIVE Reanalysis RMSV000000354.10796 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CAT [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/c5jh3d87q
title: MassIVE Reanalysis RMSV000000354.10972 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, WDR49 [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/c5jh3d886
title: MassIVE Reanalysis RMSV000000354.11181 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DEPDC5 [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/c5jh3d89p
title: MassIVE Reanalysis RMSV000000354.11359 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HTR2C [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/c5jh3d90s
title: MassIVE Reanalysis RMSV000000354.11564 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ELF1 [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.