cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5rx93m5s
title: MassIVE Reanalysis RMSV000000355.4503 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ORAI1 [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.
DOI: 10.25345/c5rx93m68
title: MassIVE Reanalysis RMSV000000355.4892 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C16orf57 [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.
DOI: 10.25345/c5rx93m7r
title: MassIVE Reanalysis RMSV000000355.5277 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C17orf47 [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.
DOI: 10.25345/c5rx93m87
title: MassIVE Reanalysis RMSV000000355.5486 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DHX33 [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.
DOI: 10.25345/c5rx93m9q
title: MassIVE Reanalysis RMSV000000355.5666 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, LOXL1 [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.
DOI: 10.25345/c5rx93n0t
title: MassIVE Reanalysis RMSV000000355.5873 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CRISP1 [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.
DOI: 10.25345/c5rx93n19
title: MassIVE Reanalysis RMSV000000355.6260 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MAGEB2 [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.
DOI: 10.25345/c5rx93n2s
title: MassIVE Reanalysis RMSV000000355.6647 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PRM3 [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.
DOI: 10.25345/c5rx93n38
title: MassIVE Reanalysis RMSV000000355.7034 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C7orf59 [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.
DOI: 10.25345/c5rx93n4r
title: MassIVE Reanalysis RMSV000000355.7249 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C7 [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.
DOI: 10.25345/c5rx93n57
title: MassIVE Reanalysis RMSV000000355.7428 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ARF6 [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.
DOI: 10.25345/c5rx93n6q
title: MassIVE Reanalysis RMSV000000355.7635 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PMEPA1 [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.
DOI: 10.25345/c5rx93n76
title: MassIVE Reanalysis RMSV000000355.7813 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TSSC4 [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.
DOI: 10.25345/c5rx93n8p
title: MassIVE Reanalysis RMSV000000355.8023 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, AFAP1L1 [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.
DOI: 10.25345/c5rx93n95
title: MassIVE Reanalysis RMSV000000355.8409 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CYB561D2 [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.
DOI: 10.25345/c5rx93p08
title: MassIVE Reanalysis RMSV000000355.8796 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GIP [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.
DOI: 10.25345/c5rx93p1r
title: MassIVE Reanalysis RMSV000000446.13 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080839/PXD004981 [9 out of 11] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5rx93p27
title: MassIVE Reanalysis RMSV000000675.57 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000090571 Chemical phosphoproteomics reveals kinase network topologies associated to genotypes and phenotypes of cancer cells [Cohort: MCF7_AZD8055] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5rx93p3q
title: MassIVE Reanalysis RMSV000000467.3 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080263/PXD003595 [1 out of 2] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5rx93p46
title: MassIVE Reanalysis RMSV000000399.15 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080692/PXD002516 [2 out of 10] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5rx93p5p
title: MassIVE Reanalysis RMSV000000384.39 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081563 HeLa proteome, CellLine_A549_46_fractions_rep1 [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5rx93p65
title: MassIVE Reanalysis RMSV000000415.9 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080794/PXD001339 [3 out of 5] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5rx93p7n
title: MassIVE MSV000091019 - Roth_Isoforms_BioID_VS30to33_2023
title: BioID data for Chtop and Sap30bp associated with the manuscript by Roth et al. 2023 describing the identification and characterization of neural alternative splicing events and associated PPI changes for 17 gene regulatory factors.
DOI: 10.25345/c5s17sx3q
title: MassIVE MSV000089805 - Integrated and high-throughput approach for sensitive analysis of tyrosine phosphoproteome
title: Tyrosine phosphorylation (pTyr) regulates various signaling pathways under normal and cancerous states. Due to their low abundance, transient, and dynamic natures, systematic profiling of pTyr sites is challenging. Antibody- and engineered-binding domain-based approaches have been well applied to pTyr peptide enrichment. However, traditional methods have the disadvantages of a long sample preparation process, which makes them unsuitable for processing a limited amount of samples, especially in a high-throughput manner. In this study, we developed a 96-well microplate-based approach to integrating all the sample preparation steps starting from cell culture to MS-compatible pTyr peptide enrichment in three consecutive 96-well microplates. By assembling the engineered SH2 domain onto a microplate, non-specific adsorption of phosphopeptides is greatly reduced, which allows us to remove the Ti-IMAC purification and three C18 desalting steps (after digestion, superbinder enrichment, and Ti-IMAC purification), and therefore greatly simplify the entire pTyr peptide enrichment workflow, especially when processing a large number of samples. Starting with 96-well microplate-cultured cells, our approach could enrich 21% more pTyr sites than the traditional serial pTyr enrichment approach and showed good sensitivity and reproducibility in the range of 200 ng to 200 ug peptides. Importantly, we applied this approach to profile tyrosine kinase inhibitors-mediated EGFR signaling pathway and could well differentiate the distinct response of different pTyr sites. Collectively, the integrated 96-well microplate-based approach is valuable for profiling pTyr sites from limited biological samples and in a high-throughput manner.
DOI: 10.25345/c5s17sx46
title: MassIVE MSV000090191 - Quantitative proteomics of ECM1-knockdown mouse kidney after chronic kidney disease
title: Mouse kidney tissues were homogenized in PBS with HALT protease inhibitor mixture (Pierce), and then boiled with SED lysis buffer (4% SDS, 50 mm EDTA, 20 mm DTT, 2% Tween 20, 100 mm Tris-HCl, pH 8.0). The proteins were digested using the Suspension Trapping (STrap) approach with in-house packed glass fiber filters (GF/F, Whatman) followed desalting using the spinnable StageTip protocol. The LC-MS/MS analysis was performed using an Orbitrap Eclipse MS (Thermo Scientific) coupled with an Ultimate 3000 nanoLC system and a FAIMS Pro Interface (Thermo Scientific). Peptides were first loaded onto a trap column and then separated by an analytical column (PepMap C18, 3.0 um; 15 cm x 75mm I.D.; Thermo Scientific) at 300 nl/min flow rate using a binary buffer system (buffer A, 0.1% formic acid in water; buffer B, 0.1% formic acid in acetonitrile) with a 165-min gradient (1% to 10% in 8 min; then to 25% buffer B over 117 min; 25% to 32% buffer B in 10 min, then to 95% buffer B over 3 min; back to 1% B in 5 min, and stay equilibration at 1% B for 20 min). Multiple CVs (-40, -60 and -80) were applied for FAIMS separation. For all experiments, the survey scans (MS1) were acquired at a resolution of 60,000 in the Orbitrap. The maximum injection time was set to Auto, and AGC target was set to Standard. Monoisotopic peak selection was set to Peptides, and the charge state filter was set to 2-7. For MS/MS acquisition, precursors were isolated with a width of 1.6 m/z, fragmented with HCD using 30% collision energy with a maximum injection time of 50 ms, and collected in Orbitrap at 15,000 resolution. The dynamic exclusion was set to 30 s, and can be shared across different FAIMS experiments. Protein identification and quantitation were performed using the Proteome Discoverer software (version 2.5, Thermo Scientific) with most of the default parameters. An Arabidopsis thaliana database; 40,668 sequences) was used for the protein identification. Other parameters include: trypsin as an enzyme with maximally two missed cleavage sites; acetylation (protein N-terminal and Lys), oxidation (Met), and phosphorylation (Ser, Thr, Tyr) as variable modifications; cysteine carbamidomethylation as a fixed modification; peptide length must be at least 7 amino acids; false discovery rate (FDR) were set at 1% for both protein and peptide identification.
DOI: 10.25345/c5s17sx5p
title: MassIVE MSV000090237 - Quantitative Proteomics Analysis of the role of COP1 in Melanoma
title: Analysis of mouse and human cell lines with TMT10-plex reagents. Cellular modifications or treatments used to understand the role of COP1 in melanoma.
DOI: 10.25345/c5s17sx65
title: MassIVE Reanalysis RMSV000000666.49 - CCMS ProteoCarta Maestro reanalysis of Zea mays from Growth heterosis in maize is associated with expression heterosis of chloroplast ribosomes (Mixture DayNight_Night) [launched by 25d00eb062cf42859106267f298c2eec]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Zea mays (Mixture DayNight_Night) from MSV000085916.
DOI: 10.25345/c5s17sx7n
title: MassIVE MSV000090415 - GNPS - MTBLS874: Marine Biodiscovery Ireland 2017 Samples / BDV10023 Aplidium pallidum
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 squirt Aplidium pallidum. Files are part of the Metabolights dataset MTBLS874.
DOI: 10.25345/c5s17sx84
title: MassIVE MSV000090621 - Leishmania TORC1 links nutrient availability to differentiation into infective
title: Leishmania TORC1 links nutrient availability to differentiation into infective
DOI: 10.25345/c5s17sx9m
title: MassIVE Reanalysis RMSV000000354.5927 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NFIL3 [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.