cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c53t9df1d
title: MassIVE Reanalysis RMSV000000355.5762 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C1orf174 [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/c53t9df2w
title: MassIVE Reanalysis RMSV000000355.5940 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TRPA1 [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/c53t9df3c
title: MassIVE Reanalysis RMSV000000355.6149 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C15orf43 [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/c53t9df4v
title: MassIVE Reanalysis RMSV000000355.6536 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SKA2 [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/c53t9df5b
title: MassIVE Reanalysis RMSV000000355.6922 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, UBE2V1 [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/c53t9df6t
title: MassIVE Reanalysis RMSV000000355.7314 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SLC47A1 [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/c53t9df79
title: MassIVE Reanalysis RMSV000000355.7526 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TSPAN8 [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/c53t9df8s
title: MassIVE Reanalysis RMSV000000355.7702 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C6orf174 [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/c53t9df98
title: MassIVE Reanalysis RMSV000000355.7911 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, UMODL1 [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/c53t9dg0c
title: MassIVE Reanalysis RMSV000000355.8298 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ASPN [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/c53t9dg1v
title: MassIVE Reanalysis RMSV000000355.8684 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SLC25A47 [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/c53t9dg2b
title: MassIVE Reanalysis RMSV000000391.9 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080858/PXD003550 [3 out of 7] [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/c53t9dg3t
title: MassIVE Reanalysis RMSV000000676.29 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081739 Pharmacoproteomic characterisation of human colon and rectal cancer - CPTAC Full Proteomes [Cohort: CMS3, BioReplicate: Sample_9G] [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/c53t9dg49
title: MassIVE Reanalysis RMSV000000681.30 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000084248 Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer [Notes: Proteome, Mixture: TCGA_C8-A12P_BH-A0C1_A2-A0EY_117C_W_BI_20131202_H-PM] [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/c53t9dg5s
title: MassIVE Reanalysis RMSV000000676.50 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081739 Pharmacoproteomic characterisation of human colon and rectal cancer - CPTAC Full Proteomes [Cohort: CMS3, BioReplicate: Sample_4C] [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/c53t9dg68
title: MassIVE Reanalysis RMSV000000456.8 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080767/PXD001129 [1 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/c53t9dg7r
title: MassIVE Reanalysis RMSV000000675.172 - 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: HL60_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/c53t9dg87
title: MassIVE Reanalysis RMSV000000370.40 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000082644 Proteomics, post-translational modifications, and integrative analyses reveal heterogeneity of molecular mechanisms within medulloblastoma subgroups [Mixture: Fractionated_Phosphoproteome_Plex02] [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/c53t9dg9q
title: MassIVE MSV000091290 - Bone collagen from South African rodent species identification using Zooarchaeology by Mass Spectrometry (ZooMS)
title: The dataset is for identification of MALDI markers for peptide mass fingerprinting of bone collagen for species identification using ZooMS. Corresponding MALDI data can be found through Zenodo at [ADD]. This dataset contatins: - raw files - peak list files - results files final confirmation biomarker searches - databases for the whole proteome, de novo marker development, and confirmation biomarker searches - csv file with information about the sample number
DOI: 10.25345/c53x83q3w
title: MassIVE Reanalysis RMSV000000664.1 - Spectra annotations obtained with Cardinal software
title: The raw data contains multiple individual tissues with different digestion times, digestion states and tissue types. Cardinal software was used to generate a table with all coordinates and their corresponding metadata. The different tissue types were manually annotated using the interactive selectROI function from Cardinal.
DOI: 10.25345/c53x83q4c
title: MassIVE MSV000090080 - GNPS - Marine heterotroph isolates for microbeMASST
title: A selection of marine heterotroph isolates. Isolates were grown overnight in marine broth and extracted in cold methanol (1:1). Samples were run on a data dependent method to contribute to microbeMASST.
DOI: 10.25345/c53x83q5v
title: MassIVE Reanalysis RMSV000000668.191 - CCMS ProteoCarta MS-GF+ reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Female_Eyes_phosphoproteome) [launched by 148d2da0ae3046aeb7af52e0653a7b24]
title: CCMS ProteoCarta database search (MSGF+) reanalysis of Mus musculus (Female_Eyes_phosphoproteome) (MSV000089856/PXD030983).
DOI: 10.25345/c53x83q6b
title: MassIVE Reanalysis RMSV000000309.4 - Open modification searching of SARS-CoV-2-human protein interaction data with MSFragger
title: We performed a reanalysis of a SARS-CoV-2-human protein-protein interaction map from MSV000085144/PXD018117. With open modification searching (OMS) any type of PTM can be identified in an unbiased fashion, without the need to explicitly specify a limited number of variable modifications. This makes it possible to explore the general presence of PTMs in the context of the SARS-CoV-2 virus-host interactome. The reanalysis with ANN-SoLo (RMSV000000359.1) resulted in an over two-fold increase in identified spectra. Based on these identifications, our detected protein interactions showed a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. Additionally, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. This reanalysis with MSFragger showed a decent overlap with the results from ANN-SoLo, illustrating that our results are not unique to ANN-SoLo and that a similar analysis could also be done with alternative OMS tools. In the original study affinity purification was performed using 27 SARS-CoV-2 proteins that were individually tagged and expressed in triplicate in HEK-293T cells. Bead-bound proteins were denatured, reduced, carbamidomethylated, and enzymatically digested using trypsin, and each sample was injected via an Easy-nLC 1200 (Thermo Fisher Scientific) into a Q-Exactive Plus mass spectrometer (Thermo Fisher Scientific). The SARS-CoV-2 proteins that were included are: all mature nonstructural proteins (Nsps), except for Nsp3 and Nsp16; a mutated version of Nsp5 to disable its proteolytic activity (Nsp5_C145A); and all predicted SARS-CoV-2 open reading frames (Orfs), including the spike (S), membrane (M), nucleocapsid (N), and envelope (E) protein. First, the downloaded raw files were converted to MGF files using ThermoRawFileParser (version 1.2.3). Next, OMS was performed using MSFragger (version 3.5) and FragPipe (version 18.0) against a concatenated FASTA file containing human protein sequences (Uniprot reviewed sequences downloaded on 2020/02/28), the SARS-CoV-2 protein sequences (version 2020/03/05), and the green fluorescent protein sequence. An equal number of decoy protein sequences were generated using FragPipe. The MSFragger search settings included a precursor mass tolerance between -150 Da and 500 Da, a fragment mass tolerance of 0.02 Da, and trypsin cleavage with up to two missed cleavages. Cysteine carbamidomethylation was used as a fixed modification, and oxidation of methionine and N-terminal acetylation were used as variable modifications. Other search settings were kept at their default values. PSMs were processed using PeptideProphet (version 4.4.0) with the FragPipe default settings for open searches and filtered at 1% FDR.
DOI: 10.25345/c53x83q7t
title: MassIVE MSV000090512 - Streptomyces sp. AF-0070_BPM-LLE_POS
title: AF-0070 was culture in BPM and extracted with EtOAC. Then, crude extraction was analyzed with LC-HRMS/MS.
DOI: 10.25345/c53x83q89
title: MassIVE MSV000090688 - Optimisation strategies for acquiring and analysing data-independent acquisition on linear ion traps for single-cell proteomics experiments
title: Optimisation strategies for acquiring and analysing data-independent acquisition on linear ion traps for low-input experiments
DOI: 10.25345/c53x83q9s
title: MassIVE MSV000090895 - Untargeted proteomics based approach to protein expression patterns by the use of MAXQUANT
title: We adopted the use of an untargeted proteomics-based approach on a 3D human brain tumor neurospheroid model for Glioblastoma exposed to drug treatment. Samples were subjected to digestion with trypsin, then analyzed by the use of a nanoflow UPLC-MS/MS for proteome comparative analysis. The detailed identification information of proteins and peptides shared for each the control and treated groups were listed in this datasest.
DOI: 10.25345/c53x83r0w
title: MassIVE Reanalysis RMSV000000354.6201 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RASGEF1A [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/c53x83r1c
title: MassIVE Reanalysis RMSV000000354.6587 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PADI3 [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/c53x83r2v
title: MassIVE Reanalysis RMSV000000354.6973 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MAX [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/c53x83r3b
title: MassIVE Reanalysis RMSV000000354.7358 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CYP7B1 [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.