cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5cj87v31
title: MassIVE Reanalysis RMSV000000355.8443 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ITGB7 [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/c5cj87v4h
title: MassIVE Reanalysis RMSV000000355.8830 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CITED1 [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/c5cj87v50
title: MassIVE Reanalysis RMSV000000382.57 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080596/PXD004242 [50 out of 51] [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/c5cj87v6g
title: MassIVE Reanalysis RMSV000000678.27 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083043 CPTAC, TCGA Cancer Proteome Study of Breast Tissue [Notes: Proteome, Mixture: 29] [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/c5cj87v7z
title: MassIVE Reanalysis RMSV000000386.20 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080864/PXD003708 [14 out of 15] [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/c5cj87v8f
title: MassIVE Reanalysis RMSV000000679.26 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086793 CPTAC LUAD Discovery Study [Notes: Proteome, Mixture: 18] [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/c5cj87v9x
title: MassIVE Reanalysis RMSV000000378.14 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080828/PXD003622 [1 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/c5cj87w01
title: MassIVE Reanalysis RMSV000000366.105 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086387 A Quantitative Proteome Map of the Human Body, TMT10 MS3 [Mixture: 50] [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/c5cj87w1h
title: MassIVE MSV000091053 - Identification of Trityl Post-translational modification by a bottom-up proteomic-based approach using UHPLC-Q Exactive Hybrid Quadrupole-Orbitrap high resolution mass spectrometry
title: We adopted a bottom-up proteomic-based approach with Tandem mass spectrometry for assessment of pesticides mixture induced neurotoxicity on human brain tumors with the aim of identification of proteins-Post translational modifications and alteration sites on peptides sequencing. Three proteins namely, Glyceraldehyde-3-phosphate-dehydrogenase (GAPDH), enolase (ENO1) and Phosphoglycerate-kinase-1 (PGK1) were selected as key targets in oxidative stress-response. Freshly resected brain tumors were cultured in neural stem-cell culture medium for a 3D neurospheroids developing model, then treated by pesticide mixture at relevant concentrations. Afterwards, proteins were extracted, reduced and alkylated, then digested by trypsin. The extracted peptides were analysed by nano-UHPLC-ESI Q Exactive HF hybrid quadrupole-Orbitrap high resolution mass spectrometry. Raw MS files were searched against human protein database based on the species of the samples using Maxquant (Version 1.6.1.14).
DOI: 10.25345/c5cn6z372
title: MassIVE MSV000089839 - GNPS_BarcelonaFontVilassar_watersamples_Negativemode_LC
title: ions detected by liquid chromatography - high resolution mass spectrometry, seawater and drinking water samples were analyzed.
DOI: 10.25345/c5cn6z38j
title: MassIVE MSV000090218 - Diversity matters: Optimal collision energies for tandem mass spectrometric analysis of a large set of N-glycopeptides - part 2
title: a) Ratio of the lower and higher energy component. Tests were done on the mixture of AGP, fetuin and transferrin digests using 2.2 pmol from all glycoproteins in each run. Five different high CE setting was used which were 50%, 75%, 100%, 125% and 150% of the original method of Hinneburg et al. These were combined with three different low CE/high CE ratio, 0.3, 0.5 and 0.7, resulting in 15 different MS/MS settings. b) Time distribution. Tests were performed on the mixture of AGP, fetuin and transferrin digests using 2.2 pmol from all glycoproteins in each run. The fraction of the MS/MS acquisition time allocated to the higher energy condition was system-atically varied from 40% to 90% in steps of 5% resulting in 10 different MS/MS methods. d) Performance check. The above energy-dependence studies allowed optimum energies to be determined for each individual N-glycopeptide, but obviously, we cannot directly apply these in practice since the identity of the glycopeptides is not known at the time of the measurement. The results on individual glycopeptides showed reasonably good m/z-dependent linear trends for the optimum energies for both Byonic and pGlyco search engines and these formed the basis for CE choice in a practical DDA measurement run. We explored the potential gain via CE optimization by comparing the number of hits using the Hinneburg et al.'s literature CE setting and our optimized MS/MS method in actual measure-ments. HeLa digest and blood plasma digest were used. The pellet fraction of acetone precipitation enriched in glycopep-tides were investigated with injection amounts of 750 ng and 1.5 ug in the case of HeLa and blood plasma, respectively. Three repetitions were carried out with each CE setting and data were evaluated using both Byonic and pGlyco search engines. e) Measurements on mAb sample. Nano-LC-MS/MS ex-periments were performed on a mAb sample using 2 pmol tryptic digest in each run. First, the energy dependence study was carried out analogously to the mixture of the 3 glycopro-tein digests and AGP tryptic digests as described above in-volving 27 nano-LC-MS/MS measurements. Then, based on the energy dependence, optimal CE method was designed for the mAb N-glycopeptides. The CE method of Hinneburg et al., the CE setting optimized for all the N-glycopeptides of the glycoprotein mixture and AGP samples and CE optimized for the mAb N-glycopeptides were tested and compared in 5-5 repetitions (15 runs overall). f) Three-stepped methods. We tested the impact of adding a third CE step at the mid-point between the high and low energy levels.
DOI: 10.25345/c5cn6z391
title: MassIVE Reanalysis RMSV000000668.326 - CCMS ProteoCarta ModDecode reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_53646) [launched by ab1ddc566e8244bd975da925e6cb9107]
title: CCMS ProteoCarta peptidoform interpretation (ModDecode) of Maestro open modification search results for Mus musculus (Cell_line_53646) from MSV000089856/PXD030983.
DOI: 10.25345/c5cn6z404
title: MassIVE MSV000090448 - Vulval Lichen Planus Proteomics
title: Proteomics of Vulval Lichen Planus in humans. Data was analyzed using QExactive mass spectrometer in DDA mode.
DOI: 10.25345/c5cn6z41m
title: MassIVE MSV000090655 - Interactive effects of depth and differential irrigation on soil microbiome composition and functioning_PNNLSoilsSFA_Naylor
title: GCMS datasets for the soil depth manuscript Abstract Two factors that are well-known to influence soil microbiomes include the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil microbiome composition and functioning down the depth profile. Here, we investigated soil and wheatgrass rhizosphere microbiomes in a common field setting under four different irrigation regimes and three depths. We demonstrated that there is a significant interactive effect, where fluctuations in soil moisture more strongly influence soil microbiomes at the surface layer than in deeper layers, including for soil community composition, diversity, and for functional profiles. Meanwhile, in rhizosphere communities the influence of irrigation was similar across the different depths, although there were slight discrepancies between the two cultivars of wheatgrass used. The lessened response of deeper soil microbiomes to changes in irrigation may be due to higher incidence of slow-growing, stress-resistant microbes.
DOI: 10.25345/c5cn6z423
title: MassIVE MSV000090832 - LFQ_benchmark_artificial_batch_effect
title: LFQ benchmark from commercial digests according to Kuharev, Joerg, et al. (2015) Sample A 5%, 30%, 65% E.coli, Yeast, Human; 1ug on column Sample B 20%, 15%, 65% E.coli, Yeast, Human; 0.7ug on column Sample C Average of Sample A and B for Spectral Library by Gas-Phase Fractionationation; 1ug on column (just for completeness, I do not use GPF anymore for my applications, please use predicted libraries or use the GPF with caution). The dilution of sample B to 70% of total concentration lifts up measured log2 fold-changes by +0.5. For non-normalized data, expected log2 fold-changes are -1.5 (E.coli), +0.5(Human), +1.5 (Yeast). A perfect cross-run normalization would restore log2 fold-changes to the classical values of -2,0,+1. If a normalization does not perform as expected or over-corrects, this LFQ benchmark can show this especially on the precursor level. 30 min linear gradient on a classical nanflow trap-elute setup using Dionex3000 and Acclaim PepMap columns.
DOI: 10.25345/c5cn6z43k
title: MassIVE Reanalysis RMSV000000354.5963 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ACMSD [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/c5cn6z442
title: MassIVE Reanalysis RMSV000000354.6346 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TMEM205 [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/c5cn6z45j
title: MassIVE Reanalysis RMSV000000354.6732 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OR52W1 [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/c5cn6z461
title: MassIVE Reanalysis RMSV000000354.7116 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SPANXA1 [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/c5cn6z47h
title: MassIVE Reanalysis RMSV000000354.7324 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ERCC6L [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/c5cn6z480
title: MassIVE Reanalysis RMSV000000354.7502 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OR10H3 [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/c5cn6z49g
title: MassIVE Reanalysis RMSV000000354.7710 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TSHR [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/c5cn6z50k
title: MassIVE Reanalysis RMSV000000354.7889 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OR2S2 [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/c5cn6z512
title: MassIVE Reanalysis RMSV000000354.8096 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ENPEP [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/c5cn6z52j
title: MassIVE Reanalysis RMSV000000354.8485 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RBFOX1 [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/c5cn6z531
title: MassIVE Reanalysis RMSV000000354.8871 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SPEM1 [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/c5cn6z54h
title: MassIVE Reanalysis RMSV000000354.9261 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DOK4 [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/c5cn6z550
title: MassIVE Reanalysis RMSV000000354.9470 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SETX [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.