cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5g15td5t
title: MassIVE Reanalysis RMSV000000355.2693 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NPTX2 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5b853m12
title: MassIVE Reanalysis RMSV000000355.2700 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PI4KAP2 [launched by aea60c3352304ba6ab67140f655b6785]
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/c56h4cs8s
title: MassIVE Reanalysis RMSV000000355.2694 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ADPRHL2 [launched by aea60c3352304ba6ab67140f655b6785]
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/c52v2cc8v
title: MassIVE Reanalysis RMSV000000355.2702 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MMACHC [launched by aea60c3352304ba6ab67140f655b6785]
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/c5tb0xx91
title: MassIVE Reanalysis RMSV000000355.2697 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PIF1 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5z31nr48
title: MassIVE Reanalysis RMSV000000355.2705 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RTP1 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5pk07446
title: MassIVE Reanalysis RMSV000000355.2701 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ARPM1 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5js9hb0h
title: MassIVE Reanalysis RMSV000000355.2704 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GAGE8 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5f18sh62
title: MassIVE Reanalysis RMSV000000355.2703 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GPR137C [launched by aea60c3352304ba6ab67140f655b6785]
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/c59882q3s
title: MassIVE Reanalysis RMSV000000355.2706 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GPR113 [launched by aea60c3352304ba6ab67140f655b6785]
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/c51v5bg8m
title: MassIVE Reanalysis RMSV000000355.2708 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZNF148 [launched by aea60c3352304ba6ab67140f655b6785]
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/c55m6292c
title: MassIVE Reanalysis RMSV000000355.2709 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TLR8 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5sb3x18q
title: MassIVE Reanalysis RMSV000000355.2712 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C9orf40 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5x34mv22
title: MassIVE Reanalysis RMSV000000355.2707 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HIST1H2BI [launched by aea60c3352304ba6ab67140f655b6785]
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/c5ht2gf0t
title: MassIVE Reanalysis RMSV000000355.2710 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C2orf50 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5nk3674z
title: MassIVE Reanalysis RMSV000000355.2698 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, USP54 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5d21rm7v
title: MassIVE Reanalysis RMSV000000355.2711 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, BEX5 [launched by aea60c3352304ba6ab67140f655b6785]
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/c58c9r64x
title: MassIVE Reanalysis RMSV000000355.2718 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PSD4 [launched by aea60c3352304ba6ab67140f655b6785]
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/c54m91d1n
title: MassIVE Reanalysis RMSV000000355.2716 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C6orf129 [launched by aea60c3352304ba6ab67140f655b6785]
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/c50v89k6d
title: MassIVE Reanalysis RMSV000000355.2717 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TSPAN16 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5w37kz1b
title: MassIVE Reanalysis RMSV000000355.2714 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C15orf32 [launched by aea60c3352304ba6ab67140f655b6785]
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/c5rb6w470
title: MassIVE Reanalysis RMSV000000355.2715 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OTX2 [launched by aea60c3352304ba6ab67140f655b6785]
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: 10.6084/m9.figshare.19312214.v1
title: Gene_Network_Variant_Dataset_mTOR_TGF_Beta.zip

description: The mTOR and TGF-b pathway genes were selected based on KEGG database (https://www.genome.jp/kegg/). Genomic sequences of the pathway genes were fetched from GRCh37 human genome database based on their genomic coordinates recorded in NCBI database (https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml).<br>Reference sequences composed of each gene sequence were used as a template to generate 400 control and 400 patient sequences for each pathway. At the first step, we created two lists of integers for both groups, thatrepresent the positions of polymorphic and pathogenic variants (‘polymorphic positions list’and ‘pathogenic positions list’). Each integer in these lists has been randomly chosen to be within certain consecutive intervals and exclusive to the other list. This interval has been set to 100 and 200 for polymorphic and pathogenic variants, respectively (Any integer within the range 1-100, 100-200, 200-300, and so on, for ‘polymorphic positions list’, and any integer within the range 1-200, 200-400, 400-600, and so on, for ‘pathogenic positions list’). In the second step, the reference base at each position represented in ‘polymorphicpositions list’ was replaced by the variant base in 40% of both control and patient sequences. The alterations in these positions were accepted as non-pathogenic and/or common variants with 0.40 minor allele frequency in both groups. In the next step, reference base at each position represented in ‘pathogenic positions list’was replaced by the variant base in 25% of control sequences and 30% of patient sequences. The alterations in these positions were accepted as disease-associated/pathogenic variants with 0.25 allele frequency in the control group and 0.30 allele frequency in the patient group. In all these steps, we set minor allele frequency (MAF) higher, because, in contrary to single-gene disorders where rare variants (with MAF&lt; 0.01) are causative, complex disorders are the consequences of the combination of the variants with higher allele frequency (MAF&gt; 0.01).All variant sequences are in haploid state.
DOI: 10.25345/c5mk65b37
title: MassIVE Reanalysis RMSV000000355.2719 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PPP1R14D [launched by aea60c3352304ba6ab67140f655b6785]
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/c5gt5fj0k
title: MassIVE Reanalysis RMSV000000355.2720 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TFAP2D [launched by aea60c3352304ba6ab67140f655b6785]
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: 10.6084/m9.figshare.19312214.v2
title: Gene_Network_Variant_Dataset_mTOR_TGF_Beta.zip

description: The mTOR and TGF-Beta pathway genes were selected based on KEGG database (https://www.genome.jp/kegg/). Genomic sequences of the pathway genes were fetched from GRCh37 human genome database based on their genomic coordinates recorded in NCBI database (https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml).<br>Reference sequences composed of each gene sequence were used as a template to generate 400 control and 400 patient sequences for each pathway. At the first step, we created two lists of integers for both groups, thatrepresent the positions of polymorphic and pathogenic variants (‘polymorphic positions list’and ‘pathogenic positions list’). Each integer in these lists has been randomly chosen to be within certain consecutive intervals and exclusive to the other list. This interval has been set to 100 and 200 for polymorphic and pathogenic variants, respectively (Any integer within the range 1-100, 100-200, 200-300, and so on, for ‘polymorphic positions list’, and any integer within the range 1-200, 200-400, 400-600, and so on, for ‘pathogenic positions list’). In the second step, the reference base at each position represented in ‘polymorphicpositions list’ was replaced by the variant base in 40% of both control and patient sequences. The alterations in these positions were accepted as non-pathogenic and/or common variants with 0.40 minor allele frequency in both groups. In the next step, reference base at each position represented in ‘pathogenic positions list’was replaced by the variant base in 25% of control sequences and 30% of patient sequences. The alterations in these positions were accepted as disease-associated/pathogenic variants with 0.25 allele frequency in the control group and 0.30 allele frequency in the patient group. In all these steps, we set minor allele frequency (MAF) higher, because, in contrary to single-gene disorders where rare variants (with MAF&lt; 0.01) are causative, complex disorders are the consequences of the combination of the variants with higher allele frequency (MAF&gt; 0.01).All variant sequences are in haploid state.
DOI: 10.25345/c5c53f39v
title: MassIVE Reanalysis RMSV000000355.2721 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, VCY [launched by aea60c3352304ba6ab67140f655b6785]
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.