cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c53n20p2p
title: MassIVE Reanalysis RMSV000000355.8151 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GNG2 [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/c53n20p35
title: MassIVE Reanalysis RMSV000000355.8329 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PCCB [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/c53n20p4n
title: MassIVE Reanalysis RMSV000000355.8539 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, KIAA1191 [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/c53n20p54
title: MassIVE Reanalysis RMSV000000355.8716 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, XYLT1 [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/c53n20p6m
title: MassIVE Reanalysis RMSV000000576.3 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080841/PXD001610 [2 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/c53n20p73
title: MassIVE Reanalysis RMSV000000584.105 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079514/PXD000561 Part 2 [23 out of 85], Liver [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/c53n20p8k
title: MassIVE Reanalysis RMSV000000494.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080640/PXD003971 [1 out of 1] [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/c53n20p92
title: MassIVE Reanalysis RMSV000000623.3 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086439 Chr18 Consortium MS-data for missing proteins mining, CID files only [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/c53n20q05
title: MassIVE Reanalysis RMSV000000416.13 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080860/PXD003902 [8 out of 8] [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/c53n20q1n
title: MassIVE Reanalysis RMSV000000508.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080076/PXD003413 [1 out of 1] [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/c53n20q24
title: MassIVE Reanalysis RMSV000000678.67 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083043 CPTAC, TCGA Cancer Proteome Study of Breast Tissue [Notes: Proteome, Mixture: 21] [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/c53n20q3m
title: MassIVE MSV000091147 - Toxoplasma ERK7 defends the apical complex from premature degradation
title: Streptavidin-bound eluent from proximity biotinylation reactions using the following Toxoplasma strains: ERK7prom-driven mVenus-BioID2: 611719, 618748, 620982; endogenously tagged ERK7-BioID2: 611721, 618750, 620984
DOI: 10.25345/c53r0px88
title: MassIVE MSV000089548 - GNPS MZMine process data resuspension test
title: data processing in MZMine for resuspension test P27
DOI: 10.25345/c53r0px9r
title: MassIVE MSV000089725 - GNPS - Untargeted metabolomics of mice BALF (treatment of ARDS with EVs)
title: Bronchoalveolar lavage fluid (BALF) collected from mice with and without the induction of Acute Respiratory Distress Syndrome (ARDS) and treated with engineered extracellular vesicles (EVs). BALF extracts were analyzed by LC-MS/MS performed in an 6545 Q-TOF LC/MS (AGILENT) using a Poroshell 120 SB-C18 reversed phase column (2.1 x 100 mm, 2.7 um)
DOI: 10.25345/c53r0pz0v
title: MassIVE MSV000089933 - Development of a Robust Score and False Discovery Rate for Metabolite Identification
title: We used machine learning (ML) to improve metabolite identification confidence in GC-MS data. This project was funded by PNNL's M/Q initiative. All data was collected on an Agilent GC 7890A coupled with a single quadrupole MSD 5975C. Metabolites were derivatized prior to analysis.
DOI: 10.25345/c53r0pz1b
title: MassIVE MSV000090111 - Bicho Mineiro (Leucoptera coffeella) descriptive analysis
title: 1234567890 1234567890 1234567890 1234567890 1234567890 1234567890 1234567890
DOI: 10.25345/c53r0pz2t
title: MassIVE Reanalysis RMSV000000668.48 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_4900) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Cell_line_4900) (MSV000089856/PXD030983).
DOI: 10.25345/c53r0pz39
title: MassIVE Reanalysis RMSV000000668.406 - CCMS ProteoCarta ModDecode reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Tongue_proteome) [launched by ab1ddc566e8244bd975da925e6cb9107]
title: CCMS ProteoCarta peptidoform interpretation (ModDecode) of Maestro open modification search results for Mus musculus (Male_Tongue_proteome) from MSV000089856/PXD030983.
DOI: 10.6084/m9.figshare.21973517
title: Evaluation of the Dimensional Changes in the Mandible, Condyles, and the Temporomandibular Joint Following Skeletal Class III Treatment with Chin Cup and Bonded Maxillary Bite Block Using Low-Dose Computed Tomography: A Single-center, Randomized Controlled Trial

description: Linear and angular measurements A new template was created from the Measure and Analyze tool of Mimics™, which was used to define the anatomical landmarks and planes and produce the desired measurements. Ikeda and Kawamura suggested that the condylar and glenoid fossa landmarks were made on the corrected sagittal view. After identifying the landmarks, the software automatically calculated the distances and the angles. Then, the data was exported in .cvs format. 3D mandibular regional superimposition and comparison analysis: The paired resulting reconstructed mandibular models were exported to 3-Matic software (3-matic13.0, Materialise NV, Leuven, Belgium), and their surfaces were warped using the Warp tool of Mimics™. Initially, The T1 and T2 3D volumes were superimposed manually by approximating similar anatomical regions of the mandible using Interactive Translate and Rotate tools of the software, followed by automatic global registration in 3-Matic software. The superimposition was repeated three times to enhance accuracy and reproducibility. The point-based analysis was performed to assess the changes in 3D mandibular models between T1 and T2, and a color map was produced to assess the mandibular shape changes. The threshold was set at 2 mm: green areas indicated differences within 2 mm (between −2 and 2 mm), red surfaces indicated positive values displacement more than 2 mm, and blue surfaces indicated negative values displacement greater than −2 mm between two 3D models. Quantitative changes were done by reporting the mean, minimum, and maximum values of part analyses on a spreadsheet and used for comparative analyses.
DOI: 10.25345/c53r0pz4s
title: MassIVE MSV000090541 - untarget analysis of sarocladium lc-ms
title: untarget analysis of sarocladium lc-ms untarget analysis of sarocladium lc-ms
DOI: 10.6084/m9.figshare.21973517.v2
title: Evaluation of the Dimensional Changes in the Mandible, Condyles, and the Temporomandibular Joint Following Skeletal Class III Treatment with Chin Cup and Bonded Maxillary Bite Block Using Low-Dose Computed Tomography: A Single-center, Randomized Controlled Trial

description: Linear and angular measurements A new template was created from the Measure and Analyze tool of Mimics™, which was used to define the anatomical landmarks and planes and produce the desired measurements. Ikeda and Kawamura suggested that the condylar and glenoid fossa landmarks were made on the corrected sagittal view. After identifying the landmarks, the software automatically calculated the distances and the angles. Then, the data was exported in .cvs format. 3D mandibular regional superimposition and comparison analysis: The paired resulting reconstructed mandibular models were exported to 3-Matic software (3-matic13.0, Materialise NV, Leuven, Belgium), and their surfaces were warped using the Warp tool of Mimics™. Initially, The T1 and T2 3D volumes were superimposed manually by approximating similar anatomical regions of the mandible using Interactive Translate and Rotate tools of the software, followed by automatic global registration in 3-Matic software. The superimposition was repeated three times to enhance accuracy and reproducibility. The point-based analysis was performed to assess the changes in 3D mandibular models between T1 and T2, and a color map was produced to assess the mandibular shape changes. The threshold was set at 2 mm: green areas indicated differences within 2 mm (between −2 and 2 mm), red surfaces indicated positive values displacement more than 2 mm, and blue surfaces indicated negative values displacement greater than −2 mm between two 3D models. Quantitative changes were done by reporting the mean, minimum, and maximum values of part analyses on a spreadsheet and used for comparative analyses.
DOI: 10.25345/c53r0pz58
title: MassIVE MSV000090925 - Synchro-PASEF allows precursor-specific fragment ion extraction and interference removal in data-independent acquisition
title: Data-independent acquisition (DIA) methods have become increasingly popular in mass spectrometry (MS)-based proteomics because they enable continuous acquisition of fragment spectra for all precursors simultaneously. However, these advantages come with the challenge of correctly reconstructing the precursor-fragment relationships in these highly convoluted spectra for reliable identification and quantification. Here we introduce a scan mode for the combination of trapped ion mobility spectrometry (TIMS) with parallel accumulation-serial fragmentation (PASEF) that seamlessly and continuously follows the natural shape of the ion cloud in ion mobility and peptide precursor mass dimensions. Termed synchro-PASEF, it increases the detected fragment ion current several-fold at sub-second cycle times. Consecutive quadrupole selection windows move synchronously through the mass and ion mobility range. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor - fragment relationships in ion mobility and mass dimensions and effectively deconvolutes the DIA fragment space. Importantly, the partitioned parts of the fragment ion transitions provide a further dimension of specificity via a lock and key mechanism. This is also advantageous for quantification, where signals from interfering precursors in the DIA selection window do not affect all partitions of the fragment ion, allowing to retain only the specific parts for quantification. Overall, we establish the defining features of synchro-PASEF and explore its potential for proteomic analyses.
DOI: 10.25345/c53r0pz6r
title: MassIVE Reanalysis RMSV000000354.6056 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HEY2 [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/c53r0pz77
title: MassIVE Reanalysis RMSV000000354.6231 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CD1E [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/c53r0pz8q
title: MassIVE Reanalysis RMSV000000354.6441 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GMNN [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/c53r0pz96
title: MassIVE Reanalysis RMSV000000354.6827 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CNPY2 [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/c53r0q00q
title: MassIVE Reanalysis RMSV000000354.7212 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CAPN6 [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/c53r0q016
title: MassIVE Reanalysis RMSV000000354.7596 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ACY1 [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/c53r0q02p
title: MassIVE Reanalysis RMSV000000354.7984 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, IDH3G [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/c53r0q035
title: MassIVE Reanalysis RMSV000000354.8193 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, BTNL8 [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/c53r0q04n
title: MassIVE Reanalysis RMSV000000354.8371 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FOXJ1 [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.