cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5610vv9m
title: MassIVE Reanalysis RMSV000000544.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080738/PXD003559 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c59s1kp32
title: MassIVE Reanalysis RMSV000000535.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080783/PXD003186 [2 out of 3] [launched by 109066555a834464860da7ed31006dcf]
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/c52805258
title: MassIVE Reanalysis RMSV000000548.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000078777 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5xg9ff1t
title: MassIVE Reanalysis RMSV000000542.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080054/PXD003411 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19178888
title: The caspofungin paradoxical effect is a tolerant "Eagle effect" in the filamentous fungal pathogen Aspergillus fumigatus

description: Cell responses against antifungals different from resistance have been rarely studied in filamentous fungi, while terms such as tolerance and persistence are well-described for bacteria and increasingly examined in yeast-like organisms. <i>Aspergillus fumigatus </i>is a filamentous fungal pathogen that causes a disease named aspergillosis and caspofungin (CAS), a fungistatic drug, used as second-line therapy. Some <i>A. fumigatus </i>clinical isolates can survive and grow in CAS concentrations above the minimum effective concentration (MEC), a phenomenon known as “caspofungin paradoxical effect” (CPE). Here we evaluated the CPE in 67 <i>A. fumigatus </i>clinical isolates by calculating the Recovery Rate (RR) value, where isolates with RR ≥ 0.1 are considered CPE<sup>+</sup> while isolates with RR &lt; 0.1 are classified as CPE<sup>-</sup>. Conidia produced by three CPE<sup>+</sup> clinical isolates, CEA17 (RR=0.42), Af293 (RR=0.59), CM7555 (RR=0.38) all showed the ability to grow in high levels of CAS while all conidia produced by the CPE<sup>-</sup> isolate IFM61407 (RR=0.00) showed no evidence of paradoxical growth. Given the importance of calcium/calcineurin/transcription factor CrzA pathway in CPE regulation, we also demonstrated that all Δ<i>crzA</i><sup>CEA17</sup> (CPE<sup>+</sup>) conidia showed CPE while 100% of Δ<i>crzA</i><sup>Af293 </sup>(CPE<sup>-</sup>) were CPE<sup>-</sup>.<sup> </sup>As all spores derived from an individual strain were phenotypically indistinct with respect to CPE it is likely that CPE is a genetically encoded adaptive trait that should be considered an antifungal tolerant phenotype. As the RR parameter shows that the strength of the CPE is not uniform between strains, we propose that the mechanisms that govern this phenomenon are multi-factorial.<sup></sup> <b> </b>
DOI: 10.25345/c5st7f11w
title: MassIVE Reanalysis RMSV000000547.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080075/PXD003414 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19178888.v1
title: Every single conidium in Aspergillus fumigatus caspofungin tolerant strains are intrinsically caspofungin tolerant

description: <i>Aspergillus fumigatus</i> is one of the most important human fungal pathogens and causes a group of human diseases named aspergillosis. Echinocandins, such as the fungistatic drug caspofungin (CAS) are used as second-line therapy. Some <i>A. fumigatus </i>clinical isolates can survive and grow in higher CAS concentrations, a phenomenon known as “caspofungin paradoxical effect” (CPE). Here we investigate if CPE is due to a subpopulation of conidia produced by a CAS tolerant strain, indicative of a persistence phenotype or is caused by all the conidia which would be consistent with a tolerance phenotype. We evaluated a set of 67 <i>A. fumigatus </i>clinical isolates for CPE growth and by using a novel CPE Index (CPEI) classified them as CPE<sup>+</sup> (CPEI ≥ 0.40) or CPE<sup>-</sup> (CPEI ≤ 0.20). Conidia produced by three CPE<sup>+</sup> clinical isolates, CEA17 (CPEI=0.52), Af293 (CPEI=0.64), CM7555 (CPEI=0.58) all showed the ability to grow in high levels of CAS while all conidia produced by the CPE<sup>-</sup> isolate IFM61407 (CPEI=0.12) strain showed no evidence of tolerance. Given the importance of calcium/calcineurin/transcription factor CrzA pathway in CPE regulation, we also evaluated Δ<i>crzA</i><sup>Af293</sup> (CPE<sup>-</sup>) and Δ<i>crzA</i><sup>CEA17</sup> (CPE<sup>+</sup>) conidia tolerance to CAS. All Δ<i>crzA</i><sup>CEA17</sup> conidia showed CPE<sup>+ </sup>while 100 % of Δ<i>crzA</i><sup>Af293</sup> spores are CPE<sup>-</sup>. As all spores derived from an individual strain are phenotypically indistinct with respect to CPE it is likely that CPE is a genetically encoded adaptive trait that should be considered an antifungal tolerant phenotype. As the CPEI shows that the strength of the CPE is not uniform between strains we propose that the mechanisms that govern this phenomenon are multi-factorial. <b></b> <b><br> </b> <b> </b>
DOI: 10.25345/c5p26q68x
title: MassIVE Reanalysis RMSV000000536.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080685/PXD004682 [2 out of 7] [launched by 109066555a834464860da7ed31006dcf]
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/c5j960d3p
title: MassIVE Reanalysis RMSV000000539.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079539/PXD000394 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5dj58k8f
title: MassIVE Reanalysis RMSV000000546.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080737/PXD004764 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c58s4js49
title: MassIVE Reanalysis RMSV000000554.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080740/PXD003324 [2 out of 2] [launched by 109066555a834464860da7ed31006dcf]
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/c5513v00w
title: MassIVE Reanalysis RMSV000000549.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000088409 Quantitative PTM Maps of Human Pathologic Tau Identify Patient Heterogeneity and Define Critical Steps in Alzheimers Disease Progression - frontal gyrus (sarkosyl soluble) [Cohort: Alzheimers_Soluble] [launched by 109066555a834464860da7ed31006dcf]
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/c51834570
title: MassIVE Reanalysis RMSV000000543.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080844/PXD004816 [4 out of 4] [launched by 109066555a834464860da7ed31006dcf]
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/c5wm13x4f
title: MassIVE Reanalysis RMSV000000550.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079947/PXD001326 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5rv0d416
title: MassIVE Reanalysis RMSV000000553.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080060/PXD004313 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5n29p96q
title: MassIVE Reanalysis RMSV000000552.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080736/PXD004796 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5cj87p7q
title: MassIVE Reanalysis RMSV000000555.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083978 2018CHPP, lysargiNase files [launched by 109066555a834464860da7ed31006dcf]
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/c5h98zh13
title: MassIVE Reanalysis RMSV000000545.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079969/PXD001421 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c57s7hw3k
title: MassIVE Reanalysis RMSV000000559.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080754/PXD004515 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5416t30n
title: MassIVE Reanalysis RMSV000000551.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080773/PXD002839 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c50c4sn96
title: MassIVE Reanalysis RMSV000000561.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080708/PXD002554 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5vm4314m
title: MassIVE Reanalysis RMSV000000562.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080048/PXD003417 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5qv3c69c
title: MassIVE Reanalysis RMSV000000558.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080277/PXD000608 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5m32nd42
title: MassIVE Reanalysis RMSV000000560.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000088407 Quantitative PTM Maps of Human Pathologic Tau Identify Patient Heterogeneity and Define Critical Steps in Alzheimers Disease Progression - frontal gyrus [Cohort: Alzheimers_Insoluble] [launched by 109066555a834464860da7ed31006dcf]
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/c5gb1xm0x
title: MassIVE Reanalysis RMSV000000563.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080796/PXD002620 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5bk16s6j
title: MassIVE Reanalysis RMSV000000565.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080712/PXD002613 [2 out of 3] [launched by 109066555a834464860da7ed31006dcf]
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/c56t0h039
title: MassIVE Reanalysis RMSV000000557.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080062/PXD002555 [1 out of 1] [launched by 109066555a834464860da7ed31006dcf]
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/c5348gk46
title: MassIVE Reanalysis RMSV000000564.1 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079014 [2 out of 2] [launched by 109066555a834464860da7ed31006dcf]
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.