cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5vq2sj3d
title: MassIVE Reanalysis RMSV000000355.5672 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DHTKD1 [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/c5vq2sj4w
title: MassIVE Reanalysis RMSV000000355.5880 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SLC16A10 [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/c5vq2sj5c
title: MassIVE Reanalysis RMSV000000355.6267 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZMYND12 [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/c5vq2sj6v
title: MassIVE Reanalysis RMSV000000355.6655 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SLC2A10 [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/c5vq2sj7b
title: MassIVE Reanalysis RMSV000000355.7041 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FLII [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/c5vq2sj8t
title: MassIVE Reanalysis RMSV000000355.7257 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SUN5 [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/c5vq2sj99
title: MassIVE Reanalysis RMSV000000355.7434 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, USP29 [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/c5vq2sk0d
title: MassIVE Reanalysis RMSV000000355.7642 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PEPD [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/c5vq2sk1w
title: MassIVE Reanalysis RMSV000000355.7821 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, IL15 [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/c5vq2sk2c
title: MassIVE Reanalysis RMSV000000355.8030 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GPR64 [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/c5vq2sk3v
title: MassIVE Reanalysis RMSV000000355.8417 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CST3 [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/c5vq2sk4b
title: MassIVE Reanalysis RMSV000000355.8803 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ATP6V1G1 [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/c5vq2sk5t
title: MassIVE Reanalysis RMSV000000681.16 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000084248 Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer [Notes: Phosphoproteome, Mixture: TCGA_A2-A0T7_C8-A12Q_A8-A079_117C_P_BI_20130905_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/c5vq2sk69
title: MassIVE Reanalysis RMSV000000586.56 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079526/PXD000865 [35 out of 46], Ascites [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/c5vq2sk7s
title: MassIVE Reanalysis RMSV000000679.16 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086793 CPTAC LUAD Discovery Study [Notes: Proteome, Mixture: 16] [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/c5vq2sk88
title: MassIVE Reanalysis RMSV000000592.57 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083508 29 tissues, tonsil Lys-N_HCD_QExactiveHF [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/c5vq2sk9r
title: MassIVE Reanalysis RMSV000000681.55 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000084248 Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer [Notes: Phosphoproteome, Mixture: TCGA_AR-A0TT_AR-A1AQ_AO-A12B_117C_P_BI_20131105_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/c5vq2sm0v
title: MassIVE Reanalysis RMSV000000373.20 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080827/PXD001856 [4 out of 10] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5vq2sm1b
title: MassIVE MSV000091026 - 01092023_PFAS_standards_CE_optimization
title: A set of 30 "forever chemicals" including sulfonates, carboxylates, sulfonamides, etc. was subjected to HPLC-MS/MS analysis to assess effects of varying collision energies and CE spreads on MS2 quality.
DOI: 10.25345/c5vt1gt7v
title: MassIVE MSV000089812 - DUX4 expression activates JNK and p38 MAP kinases in myoblasts
title: Facioscapulohumoral muscular dystrophy (FSHD) is caused by misexpression of the DUX4 transcription factor in skeletal muscle that results in transcriptional alterations, abnormal phenotypes, and cell death. To gain insight into the kinetics of DUX4-induced stresses, we activated DUX4 expression in myoblasts and performed longitudinal RNA sequencing paired with proteomics and phosphoproteomics. This analysis revealed changes in cellular physiology including DNA damage and altered mRNA splicing. Phosphoproteomic analysis uncovered widespread changes in protein phosphorylation rapidly following DUX4 induction indicating that alterations in kinase signaling may play a role in DUX4-mediated stress and cell death. Indeed, we demonstrate that two stress-responsive MAP kinase pathways, JNK and p38, are activated in response to DUX4 expression. Inhibition of each of these pathways ameliorated DUX4-mediated cell death in myoblasts. These findings uncover JNK as a novel pathway involved in DUX4-mediated cell death as well as provide additional insights into the role of the p38 pathway, a clinical target for the treatment of FSHD.
DOI: 10.25345/c5vt1gt8b
title: MassIVE MSV000090198 - PROTEOMICS AND METABOLOMICS PROFILING OF MEAT EXUDATE TO UNDERSTAND THE IMPACT OF POSTMORTEM AGING ON OXIDATIVE STABILITY OF BEEF MUSCLES
title: The objective of this study was to characterize the major proteomes and metabolites present in beef exudate and determine their relationship with the color and oxidative quality of beef muscles. Beef loin (longissimus lumborum; LD) and tenderloin (psoas major; PM) muscles were cut into sections, individually vacuum-packaged, and aged for 9, 16 and 23 days. Following aging, the meat exudates were collected and analyzed for both proteomics and metabolomics profiles. Both analyses demonstrated that distinct proteins and metabolites clustered by different muscle types and aging times were detected from meat exudate, however, metabolomics profiling presented a greater capability in identifying different aging periods. The proteome profile of PM exudate exhibited a greater concentration of oxidative metabolism enzymes, while the LD exudate contained a higher abundance of glycolytic metabolism enzymes. Greater lipid, nucleotide, carnitine and glucoside metabolites were observed in LD and 23d exudates, further explaining potential postmortem energy metabolism. HSP70 and laminin proteins, together with glucosides metabolites identified in the exudates were correlated (P&lt;0.1 and |r|&gt;0.5) to muscle oxidative stability. The results indicated that meat exudate could be a viable analytical matrix to further understand postmortem metabolism and potentially generate unique biomarker combinations to predict meat quality attributes.
DOI: 10.25345/c5vt1gt9t
title: MassIVE MSV000090241 - Secretome of HCT116 cells upon ADAM9 knockdown
title: HCT116 cells were transfected with control or ADAM9 siRNA. Twelve hours after transfection, cells were washed with PBS and cultured in serum-free medium for 48 hours. Conditioned media were collected and concentrated using Amicon Ultra-15 centrifugal filter units (MW cutoff: 3 kDa). The proteins were processed following the suspension trapping (STrap) digestion protocol using in-house packed filters (GF/F, Whatman). The peptides were desalted using the spinnable StageTip protocol. The LC-MS/MS analysis was performed using an Orbitrap Eclipse MS (Thermo Scientific) coupled with an Ultimate 3000 nanoLC system and a FAIMS Pro Interface (Thermo Scientific). Peptides were first loaded onto a trap column and then separated by an analytical column (PepMap C18, 3.0 um; 50 cm x 75mm I.D.; Thermo Scientific) at 250 nl/min flow rate using a binary buffer system (buffer A, 0.1% formic acid in water; buffer B, 0.1% formic acid in acetonitrile) with a 165-min gradient (1% to 10% in 8 min; then to 25% buffer B over 117 min; 25% to 32% buffer B in 10 min, then to 95% buffer B over 3 min; back to 1% B in 5 min, and stay equilibration at 1% B for 20 min). Multiple CVs (-40, -55 and -75) were applied for FAIMS separation. For all experiments, the survey scans (MS1) were acquired at a resolution of 60,000 in the Orbitrap. The maximum injection time was set to Auto, and AGC target was set to Standard. Monoisotopic peak selection was set to Peptides, and the charge state filter was set to 2-7. For MS/MS acquisition, precursors were isolated with a width of 1.6 m/z, fragmented with HCD using 30% collision energy with a Dynamic maximum injection time, and collected in Orbitrap at 15,000 resolution. The dynamic exclusion was set to 30 s, and can be shared across different FAIMS experiments. Protein quantitation was performed using the MaxQuant software (version 2.1.3.0) with most of the default parameters, including trypsin as an enzyme with maximally two missed cleavage sites; acetylation (protein N-terminal and Lys) and oxidation (Met) as variable modifications; cysteine carbamidomethylation as a fixed modification; peptide length must be at least 7 amino acids; false discovery rate (FDR) were set at 1% for both protein and peptide identification.
DOI: 10.25345/c5vt1gv0x
title: MassIVE Reanalysis RMSV000000670.3 - Online 2D high pH and low pH reversed phase nano LC MS/MS system for deep proteome analysis
title: Online 2D high pH and low pH reversed phase nano LC MS/MS system for deep proteome analysis
DOI: 10.25345/c5vt1gv1d
title: MassIVE MSV000090422 - GNPS - MTBLS874: Marine Biodiscovery Ireland 2017 Samples / BDV10033 Ophlitaspongia papilla
title: The outcomes of this project are to identify bioactive marine natural products from Irish marine life. This specific dataset contains LC-MS/MS spectra from tissue of the marine sponge Ophlitaspongia papilla. Files are part of the Metabolights dataset MTBLS874.
DOI: 10.25345/c5vt1gv2w
title: MassIVE MSV000090628 - Identifying biomarkers and mechanisms of toxic metal stress with global proteomics
title: Inorganic ionic mercury, Hg(II), and organomercurials, RHg(I), have differential pathophysiology in higher organisms; Hg(II) is nephrotoxic, hepatotoxic, cardiotoxic, neurotoxic, and immunotoxic whereas the common organomercurial, methylmercury, is only neurotoxic. To identify proteins forming adducts with Hg(II) or with two commonly used RHg(I) disinfectants, phenylmercuric acetate (PMA) and ethyl mercury thiosalicylate (merthiolate, MT), we applied bottom-up global proteomics to actively growing cells of the well-defined commensal bacterium Escherichia coli, briefly exposed to these toxicants. In collaboration, Sue Miller's group at UCSF devised a computational filter based on the 7 stable isotopes of Hg to reveal Hg- and RHg-modified peptide signatures in mass spectra. This algorithm successfully identified adducts in RHg-treated pure proteins and in bulk cell proteomic preparations; the latter were also benchmarked for total and protein-bound thiols, essential metals content, and free Fe. Triplicate proteomic runs yielded 768,626 peptide spectral counts including 47,828 cysteine peptide spectral counts; 8,074 of these cysteine peptides had one or more R/Hg adducts and revealed 309 proteins reproducibly binding either PMA, MT, or Hg(II). The remarkably wide reach of R/Hg toxicity was obvious in the functions of the proteins targeted by Hg(II), PMA or EtHg; multiple targets lie in glycolysis, the TCA cycle, the translational apparatus, redox damage control, and respiration, and many are highly conserved in human mitochondria. However, on a molar basis Hg(II) was more damaging to thiol homeostasis and electrolyte balance than either organomercurial, likely because, being bivalent, it can form very stable chelates with protein cysteine thiols. Recent X-ray absorption, calorimetry, and global transcriptomics also demonstrate stable chelation of Hg(II) by imino-nitrogens of thymine in DNA and implicate chelation by histidine in proteins and by uracil in RNA, respectively.
DOI: 10.25345/c5vt1gv3c
title: MassIVE Reanalysis RMSV000000354.5934 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FCGR3A [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/c5vt1gv4v
title: MassIVE Reanalysis RMSV000000354.6318 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RELB [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.