cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5c53f82q
title: MassIVE Reanalysis RMSV000000355.5405 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SPATA2 [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/c5c53f836
title: MassIVE Reanalysis RMSV000000355.5791 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CD1D [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/c5c53f84p
title: MassIVE Reanalysis RMSV000000355.6178 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, IGHG2 [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/c5c53f855
title: MassIVE Reanalysis RMSV000000355.6565 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, P2RY10 [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/c5c53f86n
title: MassIVE Reanalysis RMSV000000355.6952 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZNF473 [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/c5c53f874
title: MassIVE Reanalysis RMSV000000355.7166 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SPDYE7P [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/c5c53f88m
title: MassIVE Reanalysis RMSV000000355.7345 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, AIM1 [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/c5c53f893
title: MassIVE Reanalysis RMSV000000355.7553 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, BAD [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/c5c53f906
title: MassIVE Reanalysis RMSV000000355.7940 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TCIRG1 [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/c5c53f91p
title: MassIVE Reanalysis RMSV000000355.8326 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PLA2G5 [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/c5c53f925
title: MassIVE Reanalysis RMSV000000355.8715 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FCRL3 [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/c5c53f93n
title: MassIVE Reanalysis RMSV000000510.4 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080763/PXD004319 [3 out of 3] [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/c5c53f944
title: MassIVE Reanalysis RMSV000000384.27 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081563 HeLa proteome, CellLine_SH-SY5Y_46_fractions_rep1 [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/c5c53f95m
title: MassIVE Reanalysis RMSV000000423.4 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000078831 [1 out of 3] [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/c5c53f963
title: MassIVE Reanalysis RMSV000000675.70 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000090571 Chemical phosphoproteomics reveals kinase network topologies associated to genotypes and phenotypes of cancer cells [Cohort: HL60_KU] [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/c5c53f97k
title: MassIVE Reanalysis RMSV000000424.30 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000088398 Proteomic Atlas of the Human Brain in Alzheimers Disease [Cohort: Thalamus, Condition: Alzheimers] [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/c5c53f982
title: MassIVE Reanalysis RMSV000000470.6 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080694/PXD003562 [4 out of 4] [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/c5c53f99j
title: MassIVE Reanalysis RMSV000000477.8 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080831/PXD004915 [2 out of 4] [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/c5c53fb0n
title: MassIVE MSV000091003 - Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies
title: Raw mass spectrometry files associated with the LC-MS analysis detailed in: Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies. This work was performed to determine the site-specific N-linked glycosylation on a number of different LASV strains on recombinant protein nanoparticles.
DOI: 10.25345/c5c53fb14
title: MassIVE MSV000091145 - Species identification of Inuit archaeological skin clothing from Nuulliit, Greenland (12th -13 th cent. AD) by paleoproteomics
title: Shotgun Proteomic analysis of archaeological clothing (fur, skin, feather) from Nuulliit, Greenland (12th -13 th cent. AD)
DOI: 10.25345/c5c824j65
title: MassIVE MSV000089723 - Variation in milk proteins across lactation in Pongo pygmaeus and Gorilla gorilla
title: Milk samples from Pongo pygmaeus and Gorilla gorilla from across lactation were characterized and quantified for their protein composition.
DOI: 10.25345/c5c824j7n
title: MassIVE MSV000090109 - Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression
title: Targeted proteomics enables hypothesis-driven research by measuring the cellular expression of protein cohorts related by function, disease, or class after perturbation. Here, we present a pathway-centric approach and an assay builder resource for targeting entire pathways of proteins selected from up to 10,000 expressed proteins to directly measure their abundances, exploiting sample multiplexing to increase throughput by 16-fold. The strategy, termed GoDig, requires only a single-shot LC-MS analysis, ~1 ug combined peptide material, and real-time analytics to trigger simultaneous quantification of up to 16 samples for hundreds of analytes. We applied GoDig to quantify the impact of genetic variation on protein expression in mice fed a high-fat diet. Protein abundances were quantified for multiple protein families (e.g., kinases, lipid metabolism- and lipid droplet-associated proteins) across 480 fully-genotyped Diversity Outbred mice, revealing previously unknown protein quantitative trait loci and establishing potential linkages between specific proteins and lipid homeostasis.
DOI: 10.25345/c5c824j84
title: MassIVE Reanalysis RMSV000000668.41 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_2259) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Cell_line_2259) (MSV000089856/PXD030983).
DOI: 10.25345/c5c824j9m
title: MassIVE Reanalysis RMSV000000668.222 - CCMS ProteoCarta MS-GF+ reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Epididymis_phosphoproteome) [launched by 148d2da0ae3046aeb7af52e0653a7b24]
title: CCMS ProteoCarta database search (MSGF+) reanalysis of Mus musculus (Male_Epididymis_phosphoproteome) (MSV000089856/PXD030983).
DOI: 10.25345/c5c824k0q
title: MassIVE Reanalysis RMSV000000668.405 - CCMS ProteoCarta ModDecode reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Thymus_proteome) [launched by ab1ddc566e8244bd975da925e6cb9107]
title: CCMS ProteoCarta peptidoform interpretation (ModDecode) of Maestro open modification search results for Mus musculus (Male_Thymus_proteome) from MSV000089856/PXD030983.
DOI: 10.25345/c5c824k16
title: MassIVE MSV000090333 - An ERAD independent role for rhomboid pseudoprotease Dfm1 in mediating sphingolipid homeostasis
title: Nearly one-third of nascent proteins are initially targeted to the endoplasmic reticulum (ER) where they are correctly folded and assembled before being delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated-degradation (ERAD) removes these clients from the ER membrane to the cytosol in a process known as retrotranslocation. Our recent work demonstrates that rhomboid pseudoprotease, Dfm1, is involved in the retrotranslocation of ubiquitinated integral membrane ERAD substrates. To survey for potential interaction partners of Dfm1, we performed protein-proximity labeling by BioID (proximity-dependent biotin identification) followed by mass spectrometry and identified several interacting proteins known to play a role in the sphingolipid biosynthesis pathway. Specifically, we found that Dfm1 physically interacts with the SPOTS complex, which is composed of serine palmitoyltransferase (SPT) enzymes and accessory components and is critical for catalyzing the first rate-limiting step of the sphingolipid biosynthesis pathway. We demonstrate for the first time that Dfm1 has a role in ER export, a function that is independent of Dfm1s canonical ERAD retrotranslocation function. Specifically, we show that loss of Dfm1 results in the accumulation of phosphorylated Orm2 at the ER, suggesting a novel role for Dfm1 in controlling Orm2 export from the ER and its subsequent degradation by EGAD. Moreover, the recruitment of Cdc48 by Dfm1, which is critical for its role in ERAD retrotranslocation, is dispensable for Dfm1s role in ER export. Given that the accumulation of human Orm2 homologs, ORMDLs, is associated with many maladies, our study serves as a molecular foothold for understanding how dysregulation of sphingolipid metabolism leads to various diseases.
DOI: 10.25345/c5c824k2p
title: MassIVE MSV000090539 - Comprehensive and quantitative analysis of the changes in proteomic and phosphoproteomic profiles during stimulation and repression of steroidogenesis in MA-10 Leydig cells.
title: In the present study, we have used a quantitative LC-MS/MS approach using total and phosphopeptide-enriched proteins to identify the changes that occur in the proteome and phosphoproteome of MA-10 Leydig cells during both the stimulatory phase (Fsk/cAMP treatment) and inhibitory phase (AICAR-mediated activation of AMPK) of steroidogenesis. The phosphorylation level of several proteins, including some never before described in Leydig cells, was significantly altered during stimulation and inhibition of steroidogenesis. Our data provide new key insights into the finely tuned and dynamic processes that ensure adequate steroid hormone production.
DOI: 10.25345/c5c824k35
title: MassIVE MSV000090923 - Adaptive mRNA-loaded exosomes for targeted immunotherapy of cancer
title: To investigate the cellular mechanisms underlying nsEP-triggered exosome release, we used proteomic profiling to characterize the proteins involved in this process.
DOI: 10.25345/c5c824k4n
title: MassIVE Reanalysis RMSV000000354.6229 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HIPK2 [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/c5c824k54
title: MassIVE Reanalysis RMSV000000354.6615 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TAS2R7 [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/c5c824k6m
title: MassIVE Reanalysis RMSV000000354.6825 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ANO6 [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/c5c824k73
title: MassIVE Reanalysis RMSV000000354.7002 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ARFIP2 [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.