cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5hh6cg0f
title: MassIVE Reanalysis RMSV000000405.14 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079399 [1 out of 9] [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/c5hh6cg1x
title: MassIVE Reanalysis RMSV000000678.51 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083043 CPTAC, TCGA Cancer Proteome Study of Breast Tissue [Notes: Proteome, Mixture: 6] [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/c5hh6cg2d
title: MassIVE Reanalysis RMSV000000592.76 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083508 29 tissues, testis Trypsin_HCD_QExactiveplus [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/c5hh6cg3w
title: MassIVE MSV000091198 - Quantitative phosphoproteomics to define cAMP compartments in Human Airway Smooth Muscle cells
title: The hypothesis driving this present study is that cAMP signaling occurs in specific compartments defined primarily by the expression of distinct adenylyl cyclase (AC) isoforms. By using a direct activator of AC activity to stimulate cAMP in all pools of the cell but manipulating just one pool by overexpressing one isoform of AC at a time, we can perform subtractive analysis to determine the activated signals in a single cAMP compartment. We performed quantitative phosphoproteomics using Stable Isotope Labeling with Amino acids in Cell culture (SILAC) to identify all phosphorylated proteins in Human Airway Smooth Muscle (HASM) cells resulting from a short stimulus of AC activity. By separately overexpressing two different isoforms of AC, AC2 and AC6, that are localized in separate plasma membrane microdomains and then comparing these data to that from control cells (with their native expression of these two AC isoforms in addition to others), we can define the phosphoproteomic profile of cAMP signal emanating from each of these two compartments. Protocol: Human Airway Smooth Muscle (HASM) cells were grown in media containing 13C labeled lysine and arginine (heavy media) or in normal (light) media for 15 days. Cells were then incubated with recombinant adenoviruses expressing either lacZ, AC2, and AC6 for 24 hr. Heavy cultures of HASM cells were stimulated with 1 microM forskolin for 10 min. Lysates of treated heavy cells were mixed with lysates from vehicle-treated light cells. This created SILAC pairs for forskolin stimulation in each of the three cell conditions (lacZ, AC2, or AC6). Proteins were digested, enriched for phosphopeptides by TiO2 column, and analyzed by LC/MS/MS by the proteomics core facility at Johns Hopkins School of Medicine. The TiO2-enriched samples were run. Mass spec measured the relative abundance of a phosphopeptide when a heavy and light peptide pair (a SILAC pair) was detected in the samples. The quantitative difference represents the change in abundance of that peptide caused by the forskolin treatment. Peptide sequencing, database search, protein identification, and analysis of post-translational modifications of peptides was performed by the core. 7,000 to 10,000 confirmed phosphopeptides were detected in the enriched samples, corresponding to 2,100-2,500 unique proteins.
DOI: 10.25345/c5hm52p6z
title: MassIVE MSV000089599 - Database of chemometric analyses Saliva MALDI MS
title: MALDI (+) FT-ICR mass spectrometry (MS) combined with machine learning toward diagnostic screening in saliva for COVID-19
DOI: 10.25345/c5hm52p7f
title: MassIVE MSV000089984 - Top-down proteomics and intact protein imaging of soybean root nodules infected with Bradyrhizobium japonicum
title: Global top-down proteomics LCMS analysis of proteins purified from soybean root nodules infected with either WT or nifH- mutant Bradyrhizobium japonicum. Raw LCMS data were processed with TopPIC; combined proteoform-spectral-matches, and label free quantitation results are included as separate csv files ("*_all_PrSMs.csv", "*_LFQ_Table.csv"). Also includes MALDI-Orbitrap data of intact proteins. The MALDI raw files and xml files can be loaded into imaging software for viewing ion images. Representative summed spectra are included separately in two "IMAGE-avg11567_from100to200min.raw" files. More detailed analysis and representative proteoform ion images are discussed in the associated manuscript. For sample processing, frozen tissue were homogenized for LCMS and proteins were extracted with the MPlex protocol. For MALDI, frozen tissues were sliced and embedded on ITO slides and sprayed with DHA matrix. LCMS data were processed with TopPIC and TopPICR. Imaging data were collected with Spectroglyph software.
DOI: 10.25345/c5hm52p8x
title: MassIVE Reanalysis RMSV000000668.95 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_8248) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Cell_line_8248) (MSV000089856/PXD030983).
DOI: 10.25345/c5hm52p9d
title: MassIVE Reanalysis RMSV000000668.298 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Thymus_proteome) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Male_Thymus_proteome) (MSV000089856/PXD030983).
DOI: 10.25345/c5hm52q0h
title: MassIVE Reanalysis RMSV000000666.21 - CCMS ProteoCarta Maestro reanalysis of Zea mays from Growth heterosis in maize is associated with expression heterosis of chloroplast ribosomes (Mixture RIL_RIL317-BioRep12) [launched by 25d00eb062cf42859106267f298c2eec]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Zea mays (Mixture RIL_RIL317-BioRep12) from MSV000085916.
DOI: 10.25345/c5hm52q10
title: MassIVE MSV000090417 - GNPS - MTBLS874: Marine Biodiscovery Ireland 2017 Samples / BDV10025 Paracentrotus lividus
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 sea urchin Paracentrotus lividus. Files are part of the Metabolights dataset MTBLS874.
DOI: 10.25345/c5hm52q2g
title: MassIVE MSV000090592 - HBPE nanoparticle protein corona with Influenza A virus sera
title: Mass spectrometry data for protein corona components from Influenza A virus sera-treated HBPE nanoparticles. NP sera 1: COOH-HBPE-NP protein corona after incubation with IAV-infected sera 3 days post-infection NP sera 2: COOH-HBPE-NP protein corona after incubation with IAV-infected sera 5 days post-infection Sera 1 condition 1: whole IAV-infected sera 3 days post-infection Sera 1 condition 2: IAV-infected sera 3 days post-infection processed the same as V3 + HBPE-NP Sera 2 condition 1: whole IAV-infected sera 5 days post-infection Sera 2 condition 2: IAV-infected sera 3 days post-infection processed the same as V5 + HBPE-NP
DOI: 10.25345/c5hm52q3z
title: MassIVE MSV000090800 - Quantitative proteome and lysine succinylome characterization of lung injury induced by zinc chloride smoke inhalation in mice
title: Zinc chloride smoke inhalation is one of common resources of lung injury in military personnel and may cause severe pulmonary complications and even mortality. It is unclear how lysine succinylation (Ksucc) changed over in injured lungs induced by zinc chloride smoke inhalation. Global proteome and lysine succinylome analysis was performed on lungs with and without injury induced by inhaling zinc chloride smoke on mice to investigate the underlining molecular mechanisms. A total number of 6781 Ksucc sites were identified in lungs. The number of Ksucc sites reduced around 2000 in the injured lungs, and 91 proteins showed to have at least 5 differences in the number of Ksucc sites. 384 proteins and 749 Ksucc peptides were differentially expressed in quantitative analysis. Ksucc regulators SDH, hat1 and E2k displayed significant difference in expression which hinted important regulatory roles of these proteins in response to zinc chloride induced lung injury. Six Ksucc motifs were identified in the amino acid sequences surrounding the Ksucc sites, and Ksucc****R and Ksucc****K patterns dominated among the differentially expressed Ksucc. STRING database was used to analyze protein-protein interaction of proteins with differential expression and altered lysine succylation. A higher connectivity was shown in proteins with altered lysine succylation than the differentially expressed proteins. Highly connected proteins were mainly involved in pathways of metabolism, focal adhesion, adherens junction, reactive oxygen species, lipid and atherosclerosis, complement and coagulation cascades, DNA replication and ribosome. This work expands the understanding of molecular mechanisms of lung injury induced by zinc chloride smoke, especially form the lysine succinylation perspective and will thus facilitate future exploration of Ksucc function in human beings' lung injury.
DOI: 10.25345/c5hm52q4f
title: MassIVE Reanalysis RMSV000000354.6107 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, KIAA1267 [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/c5hm52q5x
title: MassIVE Reanalysis RMSV000000354.6491 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZBED1 [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/c5hm52q6d
title: MassIVE Reanalysis RMSV000000354.6877 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TCL1B [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/c5hm52q7w
title: MassIVE Reanalysis RMSV000000354.7086 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZNF582 [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/c5hm52q8c
title: MassIVE Reanalysis RMSV000000354.7262 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TTC29 [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/c5hm52q9v
title: MassIVE Reanalysis RMSV000000354.7471 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ASXL2 [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/c5hm52r0z
title: MassIVE Reanalysis RMSV000000354.7857 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NEU2 [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/c5hm52r1f
title: MassIVE Reanalysis RMSV000000354.8243 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GLTSCR2 [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/c5hm52r2x
title: MassIVE Reanalysis RMSV000000354.8630 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZNF408 [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/c5hm52r3d
title: MassIVE Reanalysis RMSV000000354.9017 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FAM19A1 [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/c5hm52r4w
title: MassIVE Reanalysis RMSV000000354.9228 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, POC1B [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/c5hm52r5c
title: MassIVE Reanalysis RMSV000000354.9409 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PTH1R [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/c5hm52r6v
title: MassIVE Reanalysis RMSV000000354.9613 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ALPL [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/c5hm52r7b
title: MassIVE Reanalysis RMSV000000354.9999 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HSPA9 [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/c5hm52r8t
title: MassIVE Reanalysis RMSV000000354.10386 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PSMD9 [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/c5hm52r99
title: MassIVE Reanalysis RMSV000000354.10773 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C18orf45 [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/c5hm52s0d
title: MassIVE Reanalysis RMSV000000354.10980 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SUMF2 [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.