cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5p314
title: MassIVE MSV000083218 - Polvi_yeastfilamentation_P50_VS12_SAINT3869_5600
title: Morphogenetic transitions are prevalent in the fungal kingdom. For a leading human fungal pathogen, Candida albicans, the capacity to transition between yeast and filaments is key for virulence. For the model yeast Saccharomyces cerevisiae, filamentation enables nutrient acquisition. A recent functional genomic screen in S. cerevisiae identified Mfg1 as a regulator of morphogenesis that acts in complex with Flo8 and Mss11 to mediate transcriptional responses crucial for filamentation. In C. albicans, Mfg1 also interacts physically with Flo8 and Mss11 and is critical for filamentation in response to diverse cues, but the mechanisms through which it regulates morphogenesis remained elusive. Here, we explored the consequences of perturbation of Mfg1, Flo8, and Mss11 on C. albicans morphogenesis, and identified functional divergence of complex members. We observed that C. albicans Mss11 was dispensable for filamentation, and that overexpression of FLO8 caused constitutive filamentation even in the absence of Mfg1. Harnessing transcriptional profiling and chromatin immunoprecipitation coupled to microarray analysis, we identified divergence between transcriptional targets of Flo8 and Mfg1 in C. albicans. We also established that Flo8 and Mfg1 cooperatively bind to promoters of key regulators of filamentation, including TEC1, for which overexpression was sufficient to restore filamentation in the absence of Flo8 or Mfg1. To further explore the circuitry through which Mfg1 regulates morphogenesis, we employed a novel strategy to select for mutations that restore filamentation in the absence of Mfg1. Whole genome sequencing of filamentation-competent mutants revealed chromosome 6 amplification as a conserved adaptive mechanism. A key determinant of the chromosome 6 amplification is FLO8, as deletion of one allele blocked morphogenesis, and chromosome 6 was not amplified in evolved lineages for which FLO8 was re-located to a different chromosome. Thus, this work highlights rewiring of key morphogenetic regulators over evolutionary time and aneuploidy as an adaptive mechanism driving fungal morphogenesis.
DOI: 10.25345/c5qt6k
title: MassIVE Reanalysis RMSV000000266.8 - MassIVE.quant reanalysis from offline PD results
title: This reanalysis is the statistical analysis by Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific). The data processing step in Proteome Discoverer is the same as in RMSV000000266.5. The protein report including protein abundance and statistical testing results was exported from Proteome Discoverer. The parameters when outputting the protein report from PD is the default except for Protein FDR Confidence Combined = c(High, Medium, Low) and Master = c(IsMasterProtein, IsMasterProteinCandidate). We filtered out the proteins whose Master column is IsMasterProteinCandidate so that the results have only one representative protein from each protein group. R script for extracting statistical analysis results is available in the methods folder.
DOI: 10.25345/c5ss3q
title: MassIVE MSV000083217 - Selaginella_uncinata_root
title: n-butanol peptide extract of Selaginella uncinata roots
DOI: 10.25345/c5vj0s
title: MassIVE Reanalysis RMSV000000266.7 - MassIVE.quant reanalysis from offline PD+Ratio+Median+Limma results
title: The same PSM report from Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific) in RMSV000000266.5 was used for this reanalysis. For statistical analysis, data normalization without reference channel, median protein summarization, and statistical testing using limma v3.44.1 was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script is available in the 'methods' folder.
DOI: 10.25345/c5xg7c
title: MassIVE MSV000083216 - Achyranthes_bidentata_seed
title: n-butanol peptide extract of Achyranthes bidentata seeds
DOI: 10.25345/c5zb2d
title: MassIVE Reanalysis RMSV000000268.1 - DIA-BGS-directDIA-paired t-test
title: Controlled quantitative mixtures : UPS2 protein standard spike-in into mouse cerebellum samples. The UPS2 was spiked into 10 biologically different cerebellum samples to simulate a real biological experiment with varying biological background. The sample set was measured in Biognosys facility (BGS) by directDIA method. The details are in description.pdf
DOI: 10.25345/c52441
title: MassIVE Reanalysis RMSV000000272.3 - Reanalysis of MSV000084859 - MassIVE.quant MaxQuant Identifications
title: From MaxQuant Identification in msms.txt, converted to mzTab
DOI: 10.25345/c55t6m
title: MassIVE Reanalysis RMSV000000272.1 - DIA-FLI-DIA using project-specific library : paired t-test
title: Controlled quantitative mixtures : UPS2 protein standard spike-in into mouse cerebellum samples. The UPS2 was spiked into 10 biologically different cerebellum samples to simulate a real biological experiment with varying biological background. The sample set was measured in Fritz-Lipmann-Institute (FLI) by DIA method using a project-specific library. The details are in description.pdf
DOI: 10.25345/c57s44
title: MassIVE MSV000083220 - GNPS U01 MSSA LAC in CA-MHB or RPMI+10%LB +/-Nafcillin
title: Exo-metabolomic LC/MS data of methicillin susceptible Staphyloccous aureus treated with varying concentrations of nafcillin.  Strains grown in either RPMI+10%LB or CA-MHB.
DOI: 10.25345/c59m8j
title: MassIVE Reanalysis RMSV000000271.1 - DIA-FLI-directDIA : paired t-test
title: Controlled quantitative mixtures : UPS2 protein standard spike-in into mouse cerebellum samples. The UPS2 was spiked into 10 biologically different cerebellum samples to simulate a real biological experiment with varying biological background. The sample set was measured in Fritz-Lipmann-Institute (FLI) by directDIA method. The details are in description.pdf
DOI: 10.25345/c5ck5p
title: MassIVE MSV000083221 - GNPS U01 MSSA LAC in CA-MHB or RPMI+10%LB +/-Nafcillin
title: Exo-metabolomic data for methicillin susceptible strain of LAC in CA-MHB or RPMI+10%LB +/-Nafcillin.
DOI: 10.25345/c5fb2r
title: MassIVE Reanalysis RMSV000000270.5 - CCMS Reanalysis - MSGF+ for BGS TMT
title: MassIVE.quant Identifications from Reanalysis - MassIVE.quant MSGF+
DOI: 10.25345/c5h89b
title: MassIVE MSV000083219 - GNPS U01 Staph Aureus (All strains) in CA-MHB Improved Chromatography
title: Exo-metabolomic data from all Staphylococcus aureus strains using improved chromatographic separation.  Additionally, samples diluted 10x to minimize detector saturation.
DOI: 10.25345/c5k14n
title: MassIVE Reanalysis RMSV000000270.1 - DIA-BGS-TMT with 10 fractions : paired t-test
title: Controlled quantitative mixtures : UPS2 protein standard spike-in into mouse cerebellum samples. The UPS2 was spiked into 10 biologically different cerebellum samples to simulate a real biological experiment with varying biological background. The sample set was measured in Biognosys facility (BGS) by TMT method. The details are in description.pdf
DOI: 10.25345/c5nt6z
title: MassIVE Reanalysis RMSV000000274.1 - DDA : Comparison between two groups, PAL3 vs 3
title: Comparison between two groups, Photoprobe PAL-3 and Peptide 3. Reference : Luther et al., Nature 2019
DOI: 10.25345/c5pt68
title: MassIVE Reanalysis RMSV000000269.3 - Reanalysis of MSV000084859 - MassIVE.quant MaxQuant Identifications
title: From MaxQuant Identification in msms.txt, converted to mzTab
DOI: 10.25345/c5tj1v
title: MassIVE Reanalysis RMSV000000269.1 - DIA-BGS-DIA using project-specific library : paired t-test
title: DIA-BGS-DIA using the project-specific library : paired t-test
DOI: 10.25345/c5xb1q
title: MassIVE Reanalysis RMSV000000273.1 - TMT with 10 fractions - FLI : paired t-test
title: Controlled quantitative mixtures : UPS2 protein standard spike-in into mouse cerebellum samples. The UPS2 was spiked into 10 biologically different cerebellum samples to simulate a real biological experiment with varying biological background. The sample set was measured in Fritz-Lipmann-Institute (FLI) by TMT method. The details are in description.pdf
DOI: 10.25345/c5144q
title: MassIVE Reanalysis RMSV000000276.3 - Reanalysis of MSV000084899 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000084899 - MassIVE.quant MSGF+ (Reanalysis RMSV000000276) DDA : Comparison between PAL7 vs 7
DOI: 10.25345/c54t69
title: MassIVE Reanalysis RMSV000000276.1 - DDA : Comparison between two groups, PAL7 vs 7
title: Comparison between two groups, Photoprobe PAL-7 and Peptide 7. Reference : Luther et al., Nature 2019
DOI: 10.25345/c58m87
title: MassIVE Reanalysis RMSV000000275.3 - Reanalysis of MSV000084899 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000084899 - MassIVE.quant MSGF+ (Reanalysis RMSV000000275) DDA : Comparison between two groups, PAL4 vs 4
DOI: 10.25345/c5db2f
title: MassIVE Reanalysis RMSV000000275.1 - DDA : Comparison between two groups, PAL4 vs 4
title: Comparison between two groups, Photoprobe PAL-4 and Peptide 4. Reference : Luther et al., Nature 2019
DOI: 10.25345/c5j44c
title: MassIVE Reanalysis RMSV000000274.3 - Reanalysis of MSV000084899 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000084899 - MassIVE.quant MSGF+ (Reanalysis RMSV000000273) DDA : Comparison between two groups, PAL3 vs 3
DOI: 10.25345/c5mt71
title: MassIVE Reanalysis RMSV000000278.1 - Comparison of abundances between PAL6-labeled and unlabeled LptD/E_His
title: To identify potential PAL6 binding sites, MS detectable peptides were analyzed for an altered abundance upon PAL6 photo-cross-linking. PAL6-photolabeled and unlabeled LptD/E_His protein digests were analyzed by HPLC-MS/MS in data-independent acquisition (DIA) mode for label-free quantification of LptD/EHis derived peptides. Peptides were quantified by integration of associated fragment-ion traces. Data analysis using Spectronaut software (Biognosys, Schlieren) allowed relative quantification of 335 peptides with unique amino acid sequences, 280 of which could be assigned to LptD and 55 to LptE_His. Hypothesis testing was performed by MSstats.
DOI: 10.25345/c5rm8k
title: MassIVE Reanalysis RMSV000000277.3 - Reanalysis of MSV000084897 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000084897 - MassIVE.quant MSGF+
DOI: 10.25345/c5sm8w
title: MassIVE Reanalysis RMSV000000273.4 - CCMS Reanalysis - MSGF+ for FLI TMT
title: MassIVE.quant Identifications from Reanalysis - MassIVE.quant MSGF+
DOI: 10.25345/c5wb35
title: MassIVE Reanalysis RMSV000000277.1 - Comparison between thanatin PAL5 photolabeled and untreated control E. coli
title: Comparison between two groups : Thanatin PAL5 photolabeled vs. untreated control E.coli ATCC 25922 cells
DOI: 10.25345/c5044d
title: MassIVE Reanalysis RMSV000000280.1 - DIA : BiolDS-OT dataset, Spectronaut Pulsar X
title: DIA data were analyzed with Spectronaut Pulsar X 12.0.20491.6, (Biognosys, Schlieren, Switzerland). The default settings were used for the targeted analysis of DIA data in Spectronaut. The initial mass tolerance for MS1 and MS2 was 15ppm. High precision iRT calibration was used. The analysis was performed with and without the built-in interference correction. The DDA spectra were analyzed with the MaxQuant (Version 1.5.6.5) analysis software using default settings (Trypsin/P, two missed cleavages). The search criteria included carbamidomethylation of cysteine as a fixed modification, oxidation of methionine and acetyl (protein N- terminus) as variable modifications. The initial mass tolerance for the precursor was 4.5 ppm and for the fragment ions was 20 ppm. The DDA from the BiolDS-OT dataset was searched against the UniProt fasta database (state 11.12.2014, 20,215 entries) and iRT fasta. The library was generated in Spectronaut by importing the MaxQuant search results using the default settings. . All the datasets (MP-LFC-OT, MP- SFC-OT, MP-LFC-TTOF, MP-LFC-MS1var-OT, and BiolDS-OT) were normalized based on housekeeping proteins using a global median approach for MS1 and MS2 separately. Shared peptides between the proteomes were removed. Next, Precursor and protein False Discovery Rate were set to 1%. Since the detection limit of MS1 signal was around 100, normalized MS1 intensities below 100 were considered as missing values. Precursors with any missing MS1 intensities or MS2 intensities over all the MS runs were filtered out. The R scripts for statistical analysis were available in FTP.
DOI: 10.25345/c53x7d
title: MassIVE Reanalysis RMSV000000279.3 - MaxQuant msms.txt Conversion for DDA library
title: Conversion of msms.txt from MaxQuant (Spike-in-biol-var-OT dataset DDA library)
DOI: 10.25345/c56m8m
title: MassIVE Reanalysis RMSV000000284.3 - MaxQuant msms.txt Conversion for Shotgun-ELOB
title: Conversion of the original MaxQuant msms.txt to mzTab
DOI: 10.25345/c57m8x
title: MassIVE Reanalysis RMSV000000279.1 - DIA : Spike-in-biol-var-OT dataset, Spectronaut Pulsar X
title: DIA data were analyzed with Spectronaut Pulsar X 12.0.20491.6, (Biognosys, Schlieren, Switzerland). The default settings were used for the targeted analysis of DIA data in Spectronaut. The initial mass tolerance for MS1 and MS2 was 15ppm. High precision iRT calibration was used. The analysis was performed with and without the built-in interference correction. The DDA spectra were analyzed with the MaxQuant (Version 1.5.6.5) analysis software using default settings (Trypsin/P, two missed cleavages). The search criteria included carbamidomethylation of cysteine as a fixed modification, oxidation of methionine and acetyl (protein N- terminus) as variable modifications. The initial mass tolerance for the precursor was 4.5 ppm and for the fragment ions was 20 ppm. The Spike-in-biol-var-OT DDA were searched against the mouse isoform UniProt fasta database (state 11.12.2014, 24,723 entries), and the Biognosys iRT peptides fasta database (uploaded to the public repository). TheThe library was generated in Spectronaut by importing the MaxQuant search results using the default settings. The dataset was normalized in Spectronaut Pulsar X by the default normalization option. The blood proteins ALBU_MOUSE, ALBU_HUMAN, TRFE_MOUSE, and TRFE_HUMAN, were removed due to the interference between the spiked-in proteins and the background proteins. Precursor and protein False Discovery Rate were set to 1%. Since the detection limit of MS1 signal was around 100, normalized MS1 intensities below 100 were considered as missing values. Precursors with any missing MS1 intensities or MS2 intensities over all the MS runs were filtered out. The R scripts for statistical analysis were available in FTP.
DOI: 10.25345/c5cf1s
title: MassIVE Reanalysis RMSV000000278.5 - Additional data for original submission-comparison of abundances between PAL6-labeled and unlabeled LptD/E_His
title: The result for differential analysis for the original submission and the related R script is attached.
DOI: 10.25345/c5h442
title: MassIVE Reanalysis RMSV000000278.3 - Reanalysis of MSV000084898 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000084898 - MassIVE.quant MSGF+ (Reanalysis RMSV000000278)
DOI: 10.25345/c5kx7r
title: MassIVE Reanalysis RMSV000000282.1 - DIA : MP-SFC-OT dataset, Spectronaut Pulsar X
title: DIA data were analyzed with Spectronaut Pulsar X 12.0.20491.6, (Biognosys, Schlieren, Switzerland). The default settings were used for the targeted analysis of DIA data in Spectronaut. The initial mass tolerance for MS1 and MS2 was 15ppm. High precision iRT calibration was used. The analysis was performed with and without the built-in interference correction. The DDA spectra were analyzed with the MaxQuant (Version 1.5.6.5) analysis software using default settings (Trypsin/P, two missed cleavages). The search criteria included carbamidomethylation of cysteine as a fixed modification, oxidation of methionine and acetyl (protein N- terminus) as variable modifications. The initial mass tolerance for the precursor was 4.5 ppm and for the fragment ions was 20 ppm. This dataset was normalized based on housekeeping proteins using a global median approach for MS1 and MS2 separately. Shared peptides between the proteomes were removed. Next, Precursor and protein False Discovery Rate were set to 1%. Since the detection limit of MS1 signal was around 100, normalized MS1 intensities below 100 were considered as missing values. Precursors with any missing MS1 intensities or MS2 intensities over all the MS runs were filtered out. The R scripts for statistical analysis were available in FTP. Results were used in Huang et al 2019, MSV000084864.
DOI: 10.25345/c5qm88
title: MassIVE Reanalysis RMSV000000281.1 - DIA : MP-LFC-MS1var-OT dataset, Spectronaut Pulsar X
title: DIA data were analyzed with Spectronaut Pulsar X 12.0.20491.6, (Biognosys, Schlieren, Switzerland). The default settings were used for the targeted analysis of DIA data in Spectronaut. The initial mass tolerance for MS1 and MS2 was 15ppm. High precision iRT calibration was used. The analysis was performed with and without the built-in interference correction. The DDA spectra were analyzed with the MaxQuant (Version 1.5.6.5) analysis software using default settings (Trypsin/P, two missed cleavages). The search criteria included carbamidomethylation of cysteine as a fixed modification, oxidation of methionine and acetyl (protein N- terminus) as variable modifications. The initial mass tolerance for the precursor was 4.5 ppm and for the fragment ions was 20 ppm. The MP-LFC-MS1var-OT dataset was analyzed with Spectronaut Pulsar X using default settings using the spectral libraries from Bruderer et al. This dataset was normalized based on housekeeping proteins using a global median approach for MS1 and MS2 separately. Shared peptides between the proteomes were removed. Next, Precursor and protein False Discovery Rate were set to 1%. Since the detection limit of MS1 signal was around 100, normalized MS1 intensities below 100 were considered as missing values. Precursors with any missing MS1 intensities or MS2 intensities over all the MS runs were filtered out. The R scripts for statistical analysis were available in FTP. 6 raw files from MSV000084874 were used additionally. (File names are available in annotation.csv)
DOI: 10.25345/c5vf0r
title: MassIVE Reanalysis RMSV000000280.3 - MaxQuant msms.txt Conversion for DDA library
title: Conversion of the original MaxQuant msms.txt to mzTab
DOI: 10.5285/5f3fe268651e497d936a9893f61a043a
title: Arctic Cloud Summer Expedition (ACSE): surface temperature measurements from the University of Leeds Heitronics KT15.85 infra red radiative temperature sensor on board Icebreaker Oden

description: This dataset contains surface temperature measurements from the University of Leeds' two Heitronics KT15.85 infra red radiative temperature sensors mounted on board the Swedish Icebreaker Oden durning Arctic Cloud Summer Expedition (ACSE). ACSE took place in the Arctic during summer 2014. These measurements were used to complement a suite of other observations taken during the cruise. Those of the UK contribution, as well as selected other data, are available within the associated data collection in the Centre for Environmental Data Analysis (CEDA) archives. Other cruise data may be available in the NOAA ACSE and The Bolin Centre for Climate Research SWERUS (SWEdish-Russian-US) holdings - see online resources linked to this record.

Both instruments were mounted to point to starboard, but instrument 1 pointing 45 degrees forward and instrument 2 pointing 45 degrees aft, taking raw measurements at 1Hz. The data contain both the raw measured temperature (t_meas) and a corrected value, adjusted for reflection of thermal radiation from surface. The correction follows that developed by Phil Hignett for a similar sensor on the UK Met Office C130 aircraft : MRF Tech note 28, 1988.

The Arctic Cloud Summer Expedition (ACSE) was a collaboration between the University of Leeds, the University of Stockholm, and NOAA-CIRES. ACSE aimed to study the response of Arctic boundary layer cloud to changes in surface conditions in the Arctic Ocean as a working package of the larger Swedish-Russian-US Investigation of Climate, Cryosphere and Carbon interaction (SWERUS-C3) Expedition in Summer 2014. This expedition was a core component to the overall SWERUS-C3 programme and was supported by the Swedish Polar Research Secretariat.

ACSE took place during a 3-month cruise of the Swedish Icebreaker Oden from Tromso, Norway to Barrow, Alaska and back over the summer of 2014. During this cruise ACSE scientists measured surface turbulent exchange, boundary layer structure, and cloud properties. Many of the measurements used remote sensing approaches - radar, lidar, and microwave radiometers - to retrieve vertical profiles of the dynamic and microphysical properties of the lower atmosphere and cloud.

The UK participation of ACSE was funded by the Natural Environment Research Council (NERC, grant: NE/K011820/1) and involved instrumentation from the Atmospheric Measurement Facility of the UK's National Centre for Atmospheric Science (NCAS AMF). This dataset collection contains data mainy from the UK contribution with some additional data from other institutes also archived to complement the suite of meteorological measurements.
DOI: 10.5285/ed7d19d3be8d43bbb3ae804418fb7bf4
title: Arctic Cloud Summer Expedition (ACSE): visibility and precipitation measurements from the Finnish Meteorological Institute Vaisala FD12P present weather sensor on board Icebreaker Oden

description: This dataset contains visibility and precipitation measurements from the Finnish Meteorological Institute (FMI) Vaisala FD12P present weather sensor, operated by cruise participants from Stockholm University, on board Icebreaker Oden mounted on board the Swedish Icebreaker Oden durning Arctic Cloud Summer Expedition (ACSE). These data were then prepared by Ian Brooks from the University of Leeds for inclusion in this archive.

ACSE took place in the Arctic during summer 2014. These measurements were used to complement a suite of other observations taken during the cruise. Those of the UK contribution, as well as selected other data such as these data, are available within the associated data collection in the Centre for Environmental Data Analysis (CEDA) archives. Other cruise data may be available in the NOAA ACSE and The Bolin Centre for Climate Research SWERUS (SWEdish-Russian-US) holdings - see online resources linked to this record.

Some outputs from this instrument were used as part of the quality control for some other measurements.

The Arctic Cloud Summer Expedition (ACSE) was a collaboration between the University of Leeds, the University of Stockholm, and NOAA-CIRES. ACSE aimed to study the response of Arctic boundary layer cloud to changes in surface conditions in the Arctic Ocean as a working package of the larger Swedish-Russian-US Investigation of Climate, Cryosphere and Carbon interaction (SWERUS-C3) Expedition in Summer 2014. This expedition was a core component to the overall SWERUS-C3 programme and was supported by the Swedish Polar Research Secretariat.

ACSE took place during a 3-month cruise of the Swedish Icebreaker Oden from Tromso, Norway to Barrow, Alaska and back over the summer of 2014. During this cruise ACSE scientists measured surface turbulent exchange, boundary layer structure, and cloud properties. Many of the measurements used remote sensing approaches - radar, lidar, and microwave radiometers - to retrieve vertical profiles of the dynamic and microphysical properties of the lower atmosphere and cloud.

The UK participation of ACSE was funded by the Natural Environment Research Council (NERC, grant: NE/K011820/1) and involved instrumentation from the Atmospheric Measurement Facility of the UK's National Centre for Atmospheric Science (NCAS AMF). This dataset collection contains data mainy from the UK contribution with some additional data from other institutes also archived to complement the suite of meteorological measurements.