cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/f2566ac78a664a58a23a42e9e45da788
title: Arctic Cloud Summer Expedition (ACSE): University of Leeds Mobotix camera imagery on board Icebreaker Oden

description: This dataset contains digital imagery from the University of Leed's three 'Mobotix MX-M24M IP' cameras mounted on board the Swedish Icebreaker Oden durning Arctic Cloud Summer Expedition (ACSE). ACSE took place in the Arctic during summer 2014. These imagery 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.

The three camera units were mounted pointing in the following directions:

 - Camera 1: pointing to starboard,
 - Camera 2: pointing to bow,
 - Camera 3: pointing to port.

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).
DOI: 10.5285/f2f4675203d04e4eb269e230633d03db
title: Arctic Cloud Summer Expedition (ACSE): high resolution ship motion data from the University of Leeds XSENS MTi-G-700 attitude and heading reference system on board Icebreaker Oden

description: This dataset contains high resolution attitude and motion measurements of the Icebreaker Oden ship's motion by the University of Leeds' XSENS MTi-G-700 attitude and heading reference system during the Arctic Cloud Summer Expedition (ACSE). The ACSE cruise took place in the Arctic during summer 2014. These data were obtained 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 Investigation) holdings - see online resources linked to this record.

Measurements were made at 40Hz for inertial measurements and 4Hz for GPS measurements. Though the inertial measurements were used at 20Hz when merged with sonic anemometer, 20 minute final fluxes (see related data within the parent data collection).

The XSens MTi-G-700 measures 3-axis accelerations, rotation rates, and magnetic field components as well as GPS position. Internal algorithm calculate 3-axis velocity, tilt angles and heading.  However, users of these data should note that it is often not possible to calibrate magnetic field for local platform induced distortions (soft iron and hard iron corrections) resulting in errors in magnetic field and calculated outputs. Additionally, the heading measurements were found to unreliable on the ship.

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).
DOI: 10.25345/c52x6q
title: MassIVE Reanalysis RMSV000000284.4 - MaxQuant reanalysis with id+quant mzTab
title: Reanalysis attachment with id+quant mzTab files. Please note that in order to view the analyte abundances in the mzTab file you will need to download the file by (1) clicking the "FTP Download" button on the right, (2) opening the "result" folder and (3) saving the mzTab file. Alternatively you can also download the same mzTab file by (a) clicking on the "Browse Results" button on the right, (b) clicking "Download" tab at the top of the table and (c) clicking the "Download" button in the popup panel (the mzTab file will be in the "result" folder inside the zip file).
DOI: 10.25345/c5bf1g
title: MassIVE Reanalysis RMSV000000284.1 - DDA for interactors of ELOB + MSstats
title: Digested peptide mixtures were analyzed by LC-MS/MS on a Thermo Scientific Orbitrap Fusion mass spectrometry system equipped with a Thermo Scientific Easy nLC 1200 ultra high pressure liquid chromatography and autosampler system. Samples were injected onto a C18 column (25 cm x 75 mm I.D. packed with ReproSil Pur C18 AQ 1.9 mm particles) in 0.1% formic acid and then separated with an 80 min gradient from 5% to 30% Buffer B (90% ACN/10% water/0.1% formic acid) at a flow rate of 300 nL/min. The mass spectrometer collected data in a data-dependent fashion, collecting one full scan in the Orbitrap followed by collision-induced dissociation MS/MS scans in the dual linear ion trap for the most intense peaks from the full scan with a set maximum cycle time of 3 seconds. Dynamic exclusion was enabled for 20 seconds with a repeat count of 1. Charge state screening was employed to reject analysis of singly charged species or species for which a charge could not be assigned. The raw data was analyzed using the MaxQuant algorithm (version 1.5.2.8) for the identification and quantification of peptides and proteins. Data were searched against a database containing SwissProt Human (downloaded 09/2017) sequences and HIV-1 NL4-3 sequences, concatenated to a decoy database where each sequence was randomized in order to estimate the false discovery rate (FDR). Variable modifications were allowed for methionine oxidation and protein N-terminus acet- ylation. A fixed modification was indicated for cysteine carbamidomethylation. Full trypsin specificity was required. The first search was performed with a mass accuracy of +/- 20 parts per million and the main search was performed with a mass accuracy of +/- 4.5 parts per million. A maximum of 5 modifications and 2 missed cleavages were allowed per peptide. The maximum charge was set to 7+. Individual peptide mass tolerances were allowed. For MS/MS matching, the mass tolerance was set to 0.8 Da and the top 8 peaks per 100 Da were analyzed. MS/MS matching was allowed for higher charge states, water and ammonia loss events. The data were filtered to obtain a peptide, protein, and site-level false discovery rate of 0.01. The minimum peptide length was 7 amino acids. Results were matched between runs with a time window of 2 min for biological replicates. Significant analysis was performed by MSstats to compare between each bait AP sample and infection condition to the control AP sample. The candidates were subsequently validated by targeted MS (MSV000084962).
DOI: 10.25345/c5f44f
title: MassIVE Reanalysis RMSV000000286.3 - MaxQuant msms.txt Conversion for Shotgun-CBFB
title: Conversion of the original MaxQuant msms.txt to mzTab
DOI: 10.25345/c5g44r
title: MassIVE Reanalysis RMSV000000283.1 - DIA : MP-LFC-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/c5jx62
title: MassIVE Reanalysis RMSV000000286.1 - DDA for interactors of CBFB + MSstats
title: Digested peptide mixtures were analyzed by LC-MS/MS on a Thermo Scientific Orbitrap Fusion mass spectrometry system equipped with a Thermo Scientific Easy nLC 1200 ultra high pressure liquid chromatography and autosampler system. Samples were injected onto a C18 column (25 cm x 75 mm I.D. packed with ReproSil Pur C18 AQ 1.9 mm particles) in 0.1% formic acid and then separated with an 80 min gradient from 5% to 30% Buffer B (90% ACN/10% water/0.1% formic acid) at a flow rate of 300 nL/min. The mass spectrometer collected data in a data-dependent fashion, collecting one full scan in the Orbitrap followed by collision-induced dissociation MS/MS scans in the dual linear ion trap for the most intense peaks from the full scan with a set maximum cycle time of 3 seconds. Dynamic exclusion was enabled for 20 seconds with a repeat count of 1. Charge state screening was employed to reject analysis of singly charged species or species for which a charge could not be assigned. The raw data was analyzed using the MaxQuant algorithm (version 1.5.2.8) for the identification and quantification of peptides and proteins. Data were searched against a database containing SwissProt Human (downloaded 09/2017) sequences and HIV-1 NL4-3 sequences, concatenated to a decoy database where each sequence was randomized in order to estimate the false discovery rate (FDR). Variable modifications were allowed for methionine oxidation and protein N-terminus acet- ylation. A fixed modification was indicated for cysteine carbamidomethylation. Full trypsin specificity was required. The first search was performed with a mass accuracy of +/- 20 parts per million and the main search was performed with a mass accuracy of +/- 4.5 parts per million. A maximum of 5 modifications and 2 missed cleavages were allowed per peptide. The maximum charge was set to 7+. Individual peptide mass tolerances were allowed. For MS/MS matching, the mass tolerance was set to 0.8 Da and the top 8 peaks per 100 Da were analyzed. MS/MS matching was allowed for higher charge states, water and ammonia loss events. The data were filtered to obtain a peptide, protein, and site-level false discovery rate of 0.01. The minimum peptide length was 7 amino acids. Results were matched between runs with a time window of 2 min for biological replicates. Significant analysis was performed by MSstats to compare between each bait AP sample and infection condition to the control AP sample. The candidates were subsequently validated by targeted MS (MSV000084964).
DOI: 10.25345/c5pm9b
title: MassIVE Reanalysis RMSV000000285.4 - MaxQuant reanalysis with id+quant mzTab
title: Reanalysis attachment with id+quant mzTab files. Please note that in order to view the analyte abundances in the mzTab file you will need to download the file by (1) clicking the "FTP Download" button on the right, (2) opening the "result" folder and (3) saving the mzTab file. Alternatively you can also download the same mzTab file by (a) clicking on the "Browse Results" button on the right, (b) clicking "Download" tab at the top of the table and (c) clicking the "Download" button in the popup panel (the mzTab file will be in the "result" folder inside the zip file).
DOI: 10.25345/c5tf0f
title: MassIVE Reanalysis RMSV000000285.3 - MaxQuant msms.txt Conversion for Shotgun-CUL5
title: Conversion of the original MaxQuant msms.txt to mzTab
DOI: 10.25345/c5z45g
title: MassIVE Reanalysis RMSV000000285.1 - DDA for interactors of CUL5 + MSstats
title: Digested peptide mixtures were analyzed by LC-MS/MS on a Thermo Scientific Orbitrap Fusion mass spectrometry system equipped with a Thermo Scientific Easy nLC 1200 ultra high pressure liquid chromatography and autosampler system. Samples were injected onto a C18 column (25 cm x 75 mm I.D. packed with ReproSil Pur C18 AQ 1.9 mm particles) in 0.1% formic acid and then separated with an 80 min gradient from 5% to 30% Buffer B (90% ACN/10% water/0.1% formic acid) at a flow rate of 300 nL/min. The mass spectrometer collected data in a data-dependent fashion, collecting one full scan in the Orbitrap followed by collision-induced dissociation MS/MS scans in the dual linear ion trap for the most intense peaks from the full scan with a set maximum cycle time of 3 seconds. Dynamic exclusion was enabled for 20 seconds with a repeat count of 1. Charge state screening was employed to reject analysis of singly charged species or species for which a charge could not be assigned. The raw data was analyzed using the MaxQuant algorithm (version 1.5.2.8) for the identification and quantification of peptides and proteins. Data were searched against a database containing SwissProt Human (downloaded 09/2017) sequences and HIV-1 NL4-3 sequences, concatenated to a decoy database where each sequence was randomized in order to estimate the false discovery rate (FDR). Variable modifications were allowed for methionine oxidation and protein N-terminus acet- ylation. A fixed modification was indicated for cysteine carbamidomethylation. Full trypsin specificity was required. The first search was performed with a mass accuracy of +/- 20 parts per million and the main search was performed with a mass accuracy of +/- 4.5 parts per million. A maximum of 5 modifications and 2 missed cleavages were allowed per peptide. The maximum charge was set to 7+. Individual peptide mass tolerances were allowed. For MS/MS matching, the mass tolerance was set to 0.8 Da and the top 8 peaks per 100 Da were analyzed. MS/MS matching was allowed for higher charge states, water and ammonia loss events. The data were filtered to obtain a peptide, protein, and site-level false discovery rate of 0.01. The minimum peptide length was 7 amino acids. Results were matched between runs with a time window of 2 min for biological replicates. Significant analysis was performed by MSstats to compare between each bait AP sample and infection condition to the control AP sample. The candidates were subsequently validated by targeted MS (MSV000084963).
DOI: 10.5285/0af02f899ac14c218706295d3c6d1c4d
title: Arctic Cloud Summer Expedition (ACSE): surface meteorology and radiation measurements from the Stockholm University's automatic weather station on board Icebreaker Oden

description: This dataset contains surface meteorological measurements including air temperature, relative humidity, surface irradiation and wind measurements from the Meteorologiska Institutionen Stockholms Universitet (MISU) weather station 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.

These data came from an automatic weather station installed on the 7th deck of the Icebreaker Oden, approximately 25m above the surface, measuring at 1 Hz frequency. The system was operated by Joe Sedlar who also undertook data quality control and there are several flag variables for T/RH and radiation measurements documenting known data issues - notably when primary measurements have been replaced with those from other sensors, or corrections applied. This version of the dataset was then prepared for archiving with the Centre for Environmental Data Analysis by Ian Brooks, University of Leeds.

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: 10.5285/3b1effa4b6554366b9ad571fc32a6f7d
title: Arctic Cloud Summer Expedition (ACSE): composite cloud layer data for Icebreaker Oden

description: This dataset contains derived cloud layer measurements of Icebreaker Oden utilising data from the National Centre for Atmospheric Science's Atmospheric Measurement Facility's (NCAS AMF) Halo Doppler lidar and NOAA cloud radar on board 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.

The data provide altitudes of cloud base and top for the first two cloud layers. Cloud base was established from the laser ceilometer (base of liquid cloud) whist he cloud top was established from the cloud radar data. 

Where fog was detected, the fog top altitude from the radar data is given. Note: it was possible for the radar to detect a cloud top where the laser ceilometer was not able to detecte a cloud base.

These data were prepared for archiving as NetCDF data at the Centre for Environmental Data Analysis (CEDA) by Ian Brooks, University of Leeds.

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.