cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5p44m
title: MassIVE Reanalysis RMSV000000262.3 - MassIVE.Quant-Reanalysis-Skyline-Full-Sparse-top10 features
title: Using Skyline (daily version 3.7.1.11571) first a spectral library was built using the iProphet score cut-off 0.0242 suggested in the paper as achieving 1% FDR at the PSM level, with 1031 ambiguously matched peptides excluded, resulting in 82,439 unique peptides (104,993 entries). Quantification result is the same as in RMSV000000251.2. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c5sx5v
title: MassIVE Reanalysis RMSV000000262.2 - MassIVE.Quant-Reanalysis-Skyline-Full-Sparse-top5 features
title: Using Skyline (daily version 3.7.1.11571) first a spectral library was built using the iProphet score cut-off 0.0242 suggested in the paper as achieving 1% FDR at the PSM level, with 1031 ambiguously matched peptides excluded, resulting in 82,439 unique peptides (104,993 entries). Quantification result is the same as in RMSV000000251.2. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c5xm9h
title: MassIVE Reanalysis RMSV000000262.1 - MassIVE.Quant-Reanalysis-Skyline-Full-Sparse-top3 features
title: Using Skyline (daily version 3.7.1.11571) first a spectral library was built using the iProphet score cut-off 0.0242 suggested in the paper as achieving 1% FDR at the PSM level, with 1031 ambiguously matched peptides excluded, resulting in 82,439 unique peptides (104,993 entries). Quantification result is the same as in RMSV000000251.2. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c51f1p
title: MassIVE Reanalysis RMSV000000262.8 - MassIVE.Quant-Reanalysis-Skyline-Full-50pct-top10 features
title: Using Skyline (daily version 3.7.1.11571) first a spectral library was built using the iProphet score cut-off 0.0242 suggested in the paper as achieving 1% FDR at the PSM level, with 1031 ambiguously matched peptides excluded, resulting in 82,439 unique peptides (104,993 entries). Quantification result is the same as in RMSV000000251.2. The 50% q-filter eliminated the entire LC-MS features where the q-values of over 50% of the peaks exceeded 0.01. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c5543k
title: MassIVE Reanalysis RMSV000000262.7 - MassIVE.Quant-Reanalysis-Skyline-Full-50pct-top5 features
title: Using Skyline (daily version 3.7.1.11571) first a spectral library was built using the iProphet score cut-off 0.0242 suggested in the paper as achieving 1% FDR at the PSM level, with 1031 ambiguously matched peptides excluded, resulting in 82,439 unique peptides (104,993 entries). Quantification result is the same as in RMSV000000251.2. The 50% q-filter eliminated the entire LC-MS features where the q-values of over 50% of the peaks exceeded 0.01. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c57x5w
title: MassIVE Reanalysis RMSV000000262.14 - MassIVE.Quant-Reanalysis-Skyline-LowCV-50pct-all features
title: Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup, RMSV000000251.2). Quantification result is the same as in RMSV000000251.1. The 50% q-filter eliminated the entire LC-MS features where the q-values of over 50% of the peaks exceeded 0.01. All features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c58x56
title: MassIVE Reanalysis RMSV000000262.6 - MassIVE.Quant-Reanalysis-Skyline-Full-50pct-top3 features
title: Using Skyline (daily version 3.7.1.11571) first a spectral library was built using the iProphet score cut-off 0.0242 suggested in the paper as achieving 1% FDR at the PSM level, with 1031 ambiguously matched peptides excluded, resulting in 82,439 unique peptides (104,993 entries). Quantification result is the same as in RMSV000000251.2. The 50% q-filter eliminated the entire LC-MS features where the q-values of over 50% of the peaks exceeded 0.01. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c5cm85
title: MassIVE Reanalysis RMSV000000262.13 - MassIVE.Quant-Reanalysis-Skyline-LowCV-Sparse-feature selection
title: Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup, RMSV000000251.2). Quantification result is the same as in RMSV000000251.1. Uninformative features and outliers were flagged by feature selection algorithm and removed for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c5hf11
title: MassIVE Reanalysis RMSV000000262.12 - MassIVE.Quant-Reanalysis-Skyline-LowCV-Sparse-top10 features
title: Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup, RMSV000000251.2). Quantification result is the same as in RMSV000000251.1. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c5n43x
title: MassIVE Reanalysis RMSV000000262.11 - MassIVE.Quant-Reanalysis-Skyline-LowCV-Sparse-top5 features
title: Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup, RMSV000000251.2). Quantification result is the same as in RMSV000000251.1. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c5rx5j
title: MassIVE Reanalysis RMSV000000262.10 - MassIVE.Quant-Reanalysis-Skyline-LowCV-Sparse-top3 features
title: Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup, RMSV000000251.2). Quantification result is the same as in RMSV000000251.1. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c5wm8t
title: MassIVE Reanalysis RMSV000000262.9 - MassIVE.Quant-Reanalysis-Skyline-Full-50pct-feature selection
title: Using Skyline (daily version 3.7.1.11571) first a spectral library was built using the iProphet score cut-off 0.0242 suggested in the paper as achieving 1% FDR at the PSM level, with 1031 ambiguously matched peptides excluded, resulting in 82,439 unique peptides (104,993 entries). Quantification result is the same as in RMSV000000251.2. The 50% q-filter eliminated the entire LC-MS features where the q-values of over 50% of the peaks exceeded 0.01. Uninformative features and outliers were flagged by feature selection algorithm and removed for statistical analysis in MSstats R package for this reanalysis.Details for next steps are available in description.pdf
DOI: 10.25345/c50f1c
title: MassIVE Reanalysis RMSV000000262.16 - MassIVE.Quant-Reanalysis-Skyline-LowCV-50pct-top5 features
title: Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup, RMSV000000251.2). Quantification result is the same as in RMSV000000251.1. The 50% q-filter eliminated the entire LC-MS features where the q-values of over 50% of the peaks exceeded 0.01. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c53730
title: MassIVE Reanalysis RMSV000000263.5 - MassIVE.Quant-Reanalysis-MaxQuant-top3 features
title: MS/MS spectra were searched using MaxQuant (v1.5.2.8) and Andromeda as search engine. Acquired data were searched against an in-house generated database containing all the spiked-in proteins (Supplementary Table 2), and the E. coli Swissprot protein database (November 2015 version). Precur- sor ion mass tolerance was set to 4.5 ppm at the MS1 level and to 0.5 Da at the fragment ion level. Up to three missed cleavages for trypsin were allowed. Oxidation of methionine and protein N-terminal acetylation were considered as variable modifications, whereas carbamidomethylation on cysteines was set as a fixed modification. Match between runs was activated with a matching time window of 0.7 min and an alignment time window of 20 min. False discovery rate (FDR) in peptide identification was evaluated by using a decoy database and it was set to a maximum of 1%. PSM areas were extracted with the intensity extraction algorithm of MaxQuant. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.2. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c54739
title: MassIVE Reanalysis RMSV000000262.15 - MassIVE.Quant-Reanalysis-Skyline-LowCV-50pct-top3 features
title: Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup, RMSV000000251.2). Quantification result is the same as in RMSV000000251.1. The 50% q-filter eliminated the entire LC-MS features where the q-values of over 50% of the peaks exceeded 0.01. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c56x5k
title: MassIVE Reanalysis RMSV000000263.4 - MassIVE.Quant-Reanalysis-Skyline-feature selection
title: MS/MS spectra searched using MaxQuant (v1.5.2.8) and Andromeda as search engine as described previously were imported as a spectral library with a score filter&gt;0.8. Extracted ion chromatograms were generated by Skyline daily v3.4.9.9576 within 5 min of the library retention time using 3 isotopic peaks for all peptides corresponding to the spiked-in proteins and the E.coli proteins previously identified with MaxQuant. Only peptides with charge +2 and +3 were considered. Automatic peak picking was manually reviewed for the spiked-in proteins and refined with idotp &gt; 0.75 for the E. coli proteome. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.1. Uninformative features and outliers were flagged by feature selection algorithm and removed for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5bq7h
title: MassIVE Reanalysis RMSV000000263.3 - MassIVE.Quant-Reanalysis-Skyline-top10 features
title: MS/MS spectra searched using MaxQuant (v1.5.2.8) and Andromeda as search engine as described previously were imported as a spectral library with a score filter&gt;0.8. Extracted ion chromatograms were generated by Skyline daily v3.4.9.9576 within 5 min of the library retention time using 3 isotopic peaks for all peptides corresponding to the spiked-in proteins and the E.coli proteins previously identified with MaxQuant. Only peptides with charge +2 and +3 were considered. Automatic peak picking was manually reviewed for the spiked-in proteins and refined with idotp &gt; 0.75 for the E. coli proteome. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.1. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5gf0b
title: MassIVE Reanalysis RMSV000000263.2 - MassIVE.Quant-Reanalysis-Skyline-top5 features
title: MS/MS spectra searched using MaxQuant (v1.5.2.8) and Andromeda as search engine as described previously were imported as a spectral library with a score filter&gt;0.8. Extracted ion chromatograms were generated by Skyline daily v3.4.9.9576 within 5 min of the library retention time using 3 isotopic peaks for all peptides corresponding to the spiked-in proteins and the E.coli proteins previously identified with MaxQuant. Only peptides with charge +2 and +3 were considered. Automatic peak picking was manually reviewed for the spiked-in proteins and refined with idotp &gt; 0.75 for the E. coli proteome. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.1. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5m728
title: MassIVE Reanalysis RMSV000000263.1 - MassIVE.Quant-Reanalysis-Skyline-top3 features
title: MS/MS spectra searched using MaxQuant (v1.5.2.8) and Andromeda as search engine as described previously were imported as a spectral library with a score filter&gt;0.8. Extracted ion chromatograms were generated by Skyline daily v3.4.9.9576 within 5 min of the library retention time using 3 isotopic peaks for all peptides corresponding to the spiked-in proteins and the E.coli proteins previously identified with MaxQuant. Only peptides with charge +2 and +3 were considered. Automatic peak picking was manually reviewed for the spiked-in proteins and refined with idotp &gt; 0.75 for the E. coli proteome. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.1. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5qx6m
title: MassIVE Reanalysis RMSV000000262.18 - MassIVE.Quant-Reanalysis-Skyline-LowCV-50pct-feature selection
title: Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup, RMSV000000251.2). Quantification result is the same as in RMSV000000251.1. The 50% q-filter eliminated the entire LC-MS features where the q-values of over 50% of the peaks exceeded 0.01. Uninformative features and outliers were flagged by feature selection algorithm and removed for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c5vq75
title: MassIVE Reanalysis RMSV000000262.17 - MassIVE.Quant-Reanalysis-Skyline-LowCV-50pct-top10 features
title: Using Skyline (daily version 3.7.1.11571) and starting from the settings for the broadly inclusive test, we restored semi-tryptic cleavage and the variable modification Oxidation (M), expecting unstable peptides to be filtered by our first experiment(Reanalysis-Skyline-all-nodup, RMSV000000251.2). Quantification result is the same as in RMSV000000251.1. The 50% q-filter eliminated the entire LC-MS features where the q-values of over 50% of the peaks exceeded 0.01. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis. Details for next steps are available in description.pdf
DOI: 10.25345/c59q8k
title: MassIVE Reanalysis RMSV000000263.11 - MassIVE.Quant-Reanalysis-Progenesis-top10 features
title: Peptide features were identified with the Progenesis QI v4.0 algorithm, aligned across all files, and annotated with the peptide identification resulting from the database search result from Proteome Discovery and Mascot. Unique tryptic peptides corresponding to the spiked-in proteins were quantified using the feature areas as calculated by the Progenesis algorithm. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.3. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5ff01
title: MassIVE Reanalysis RMSV000000263.10 - MassIVE.Quant-Reanalysis-Progenesis-top5 features
title: Peptide features were identified with the Progenesis QI v4.0 algorithm, aligned across all files, and annotated with the peptide identification resulting from the database search result from Proteome Discovery and Mascot. Unique tryptic peptides corresponding to the spiked-in proteins were quantified using the feature areas as calculated by the Progenesis algorithm. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.3. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5k73b
title: MassIVE Reanalysis RMSV000000263.9 - MassIVE.Quant-Reanalysis-Progenesis-top3 features
title: Peptide features were identified with the Progenesis QI v4.0 algorithm, aligned across all files, and annotated with the peptide identification resulting from the database search result from Proteome Discovery and Mascot. Unique tryptic peptides corresponding to the spiked-in proteins were quantified using the feature areas as calculated by the Progenesis algorithm. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.3. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5px5x
title: MassIVE Reanalysis RMSV000000263.8 - MassIVE.Quant-Reanalysis-MaxQuant-feature selection
title: MS/MS spectra were searched using MaxQuant (v1.5.2.8) and Andromeda as search engine. Acquired data were searched against an in-house generated database containing all the spiked-in proteins (Supplementary Table 2), and the E. coli Swissprot protein database (November 2015 version). Precur- sor ion mass tolerance was set to 4.5 ppm at the MS1 level and to 0.5 Da at the fragment ion level. Up to three missed cleavages for trypsin were allowed. Oxidation of methionine and protein N-terminal acetylation were considered as variable modifications, whereas carbamidomethylation on cysteines was set as a fixed modification. Match between runs was activated with a matching time window of 0.7 min and an alignment time window of 20 min. False discovery rate (FDR) in peptide identification was evaluated by using a decoy database and it was set to a maximum of 1%. PSM areas were extracted with the intensity extraction algorithm of MaxQuant. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.2. Uninformative features and outliers were flagged by feature selection algorithm and removed for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5tq7v
title: MassIVE Reanalysis RMSV000000263.7 - MassIVE.Quant-Reanalysis-MaxQuant-top10 features
title: MS/MS spectra were searched using MaxQuant (v1.5.2.8) and Andromeda as search engine. Acquired data were searched against an in-house generated database containing all the spiked-in proteins (Supplementary Table 2), and the E. coli Swissprot protein database (November 2015 version). Precur- sor ion mass tolerance was set to 4.5 ppm at the MS1 level and to 0.5 Da at the fragment ion level. Up to three missed cleavages for trypsin were allowed. Oxidation of methionine and protein N-terminal acetylation were considered as variable modifications, whereas carbamidomethylation on cysteines was set as a fixed modification. Match between runs was activated with a matching time window of 0.7 min and an alignment time window of 20 min. False discovery rate (FDR) in peptide identification was evaluated by using a decoy database and it was set to a maximum of 1%. PSM areas were extracted with the intensity extraction algorithm of MaxQuant. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.2. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5zf0p
title: MassIVE Reanalysis RMSV000000263.6 - MassIVE.Quant-Reanalysis-MaxQuant-top5 features
title: MS/MS spectra were searched using MaxQuant (v1.5.2.8) and Andromeda as search engine. Acquired data were searched against an in-house generated database containing all the spiked-in proteins (Supplementary Table 2), and the E. coli Swissprot protein database (November 2015 version). Precur- sor ion mass tolerance was set to 4.5 ppm at the MS1 level and to 0.5 Da at the fragment ion level. Up to three missed cleavages for trypsin were allowed. Oxidation of methionine and protein N-terminal acetylation were considered as variable modifications, whereas carbamidomethylation on cysteines was set as a fixed modification. Match between runs was activated with a matching time window of 0.7 min and an alignment time window of 20 min. False discovery rate (FDR) in peptide identification was evaluated by using a decoy database and it was set to a maximum of 1%. PSM areas were extracted with the intensity extraction algorithm of MaxQuant. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.2. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c52729
title: MassIVE Reanalysis RMSV000000263.13 - MassIVE.Quant-Reanalysis-ProteomeDiscoverer-top3 features
title: MS/MS spectra were searched using Proteome Discovery software suite (v1.4) and Mascot (v2.5) as search engine. Acquired data were searched against an in-house generated database containing all the spiked-in proteins (Supplementary Table 2), and the E. coli Swissprot protein database (November 2015 version). Precursor ion mass tolerance was set to 4.5 ppm at the MS1 level and to 0.5 Da at the fragment ion level. Up to three missed cleavages for trypsin were allowed. Oxidation of methionine and protein N-terminal acetylation were considered as variable modifications, whereas carbamidomethylation on cysteines was set as a fixed modification. False discovery rate (FDR) in peptide identification was evaluated by using a decoy database and it was set to a maximum of 1%. Peptide areas were extracted with the Precursor Area Ion Detector module of Proteome Discoverer with a mass tolerance of 2 ppm. The report for PSM level is used for downstream statistical analysis. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.4. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c55159
title: MassIVE Reanalysis RMSV000000264.9 - 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 RMSV000000264.7 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.