cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5t156
title: MassIVE Reanalysis RMSV000000257.16 - MassIVE.Quant-Reanalysis-OpenSWATH-feature selection
title: Data processing was performed as described in the original manuscript, Navarro et al., 2016. The outputs for fragment-level quantification were used in further analysis. Quantification result is the same as in RMSV000000250.4. 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/c5v15h
title: MassIVE Reanalysis RMSV000000257.8 - MassIVE.Quant-Reanalysis-Spectronaut-feature selection
title: Data was reanalyzed in Spectronaut 11 (11.0.15038) using default settings and the library from the original manuscript, Navarro et al., 2016. Quantification result is the same as in RMSV000000250.2. 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/c51h81
title: MassIVE Reanalysis RMSV000000258.6 - MassIVE.Quant-Reanalysis-Spectronaut-top5 features
title: A spectral library was generated using all available raw files (24 DDA files plus 24 DIA files) using the Pulsar search engine integrated in Spectronaut 11(11.0.15038) with default settings. Data processing was performed as described in the original manuscript. The uniprot human reference proteome from 2017.06.14 was used for the spectrum centric data analysis for library generation. Further included were the custom FASTA file for the spike-in proteins as well as the MaxQuant contaminants FASTA file. The resulting library was further filtered to remove all overlapping peptide sequences between the human background proteome and the spike-in proteins. DIA data was then analyzed using default settings and exported using the built in MSstats Report (v3.7.3) export schema. Quantification result is the same as in RMSV000000252.2. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c55b1w
title: MassIVE Reanalysis RMSV000000258.5 - MassIVE.Quant-Reanalysis-Spectronaut-top3 features
title: A spectral library was generated using all available raw files (24 DDA files plus 24 DIA files) using the Pulsar search engine integrated in Spectronaut 11(11.0.15038) with default settings. Data processing was performed as described in the original manuscript. The uniprot human reference proteome from 2017.06.14 was used for the spectrum centric data analysis for library generation. Further included were the custom FASTA file for the spike-in proteins as well as the MaxQuant contaminants FASTA file. The resulting library was further filtered to remove all overlapping peptide sequences between the human background proteome and the spike-in proteins. DIA data was then analyzed using default settings and exported using the built in MSstats Report (v3.7.3) export schema. Quantification result is the same as in RMSV000000252.2. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5915j
title: MassIVE Reanalysis RMSV000000258.4 - MassIVE.Quant-Reanalysis-Skyline-feature selection
title: In Skyline (version 3.7.0.11317) a new document was created with default settings, plus Oxidation (M), Acetyl (N-Term), Amonia Loss (K, N, Q, R), and Water Loss (D, E, S, T) modifications, precursor charge states 1-7 and fragment charge states 1-6, for fragment types y, b and precursor, the 6 most intense library fragment ions and chromatogram extraction was set to use 15 ppm mass tolerance applying to all centroided MS/MS spectra using the 19 variable window isolation schemed defined in the paper, with 1 m/z margins, spanning 400-1220 m/z and 10 minutes of predicted retention times using the iRT values found in the paper assay library. Quantification result is the same as in RMSV000000252.1. 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/c5dt75
title: MassIVE Reanalysis RMSV000000258.3 - MassIVE.Quant-Reanalysis-Skyline-top10 features
title: In Skyline (version 3.7.0.11317) a new document was created with default settings, plus Oxidation (M), Acetyl (N-Term), Amonia Loss (K, N, Q, R), and Water Loss (D, E, S, T) modifications, precursor charge states 1-7 and fragment charge states 1-6, for fragment types y, b and precursor, the 6 most intense library fragment ions and chromatogram extraction was set to use 15 ppm mass tolerance applying to all centroided MS/MS spectra using the 19 variable window isolation schemed defined in the paper, with 1 m/z margins, spanning 400-1220 m/z and 10 minutes of predicted retention times using the iRT values found in the paper assay library. Quantification result is the same as in RMSV000000252.1. 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/c5jh92
title: MassIVE Reanalysis RMSV000000258.2 - MassIVE.Quant-Reanalysis-Skyline-top5 features
title: In Skyline (version 3.7.0.11317) a new document was created with default settings, plus Oxidation (M), Acetyl (N-Term), Amonia Loss (K, N, Q, R), and Water Loss (D, E, S, T) modifications, precursor charge states 1-7 and fragment charge states 1-6, for fragment types y, b and precursor, the 6 most intense library fragment ions and chromatogram extraction was set to use 15 ppm mass tolerance applying to all centroided MS/MS spectra using the 19 variable window isolation schemed defined in the paper, with 1 m/z margins, spanning 400-1220 m/z and 10 minutes of predicted retention times using the iRT values found in the paper assay library. Quantification result is the same as in RMSV000000252.1. 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/c5nb17
title: MassIVE Reanalysis RMSV000000258.9 - MassIVE.Quant-Reanalysis-DIAUmpire-top3 features
title: The raw files were converted to mzXML files with centroiding. The resulting mzXML files were processed by the signal extraction (SE) module of DIA-Umpire to generate pseudo-MSMS spectra. The generated pseudo-MS/MS spectra were searched using X! Tandem, Comet and MSGF+ search engines. The output files from the search engines were further analyzed by PeptideProphet and combined by iProphet. FDR filtering was done with PeptideProphet and ProteinProphet. DIA-Umpire's Quant module was for the quantification analysis. The outputs for all-level quantification (FragSummary, PeptideSummary, ProtSummary) were used in further analysis. Quantification result is the same as in RMSV000000252.3. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5pb05
title: MassIVE Reanalysis RMSV000000258.1 - MassIVE.Quant-Reanalysis-Skyline-top3 features
title: In Skyline (version 3.7.0.11317) a new document was created with default settings, plus Oxidation (M), Acetyl (N-Term), Amonia Loss (K, N, Q, R), and Water Loss (D, E, S, T) modifications, precursor charge states 1-7 and fragment charge states 1-6, for fragment types y, b and precursor, the 6 most intense library fragment ions and chromatogram extraction was set to use 15 ppm mass tolerance applying to all centroided MS/MS spectra using the 19 variable window isolation schemed defined in the paper, with 1 m/z margins, spanning 400-1220 m/z and 10 minutes of predicted retention times using the iRT values found in the paper assay library. Quantification result is the same as in RMSV000000252.1. 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/c5s15w
title: MassIVE Reanalysis RMSV000000258.8 - MassIVE.Quant-Reanalysis-Spectronaut-feature selection
title: A spectral library was generated using all available raw files (24 DDA files plus 24 DIA files) using the Pulsar search engine integrated in Spectronaut 11(11.0.15038) with default settings. Data processing was performed as described in the original manuscript. The uniprot human reference proteome from 2017.06.14 was used for the spectrum centric data analysis for library generation. Further included were the custom FASTA file for the spike-in proteins as well as the MaxQuant contaminants FASTA file. The resulting library was further filtered to remove all overlapping peptide sequences between the human background proteome and the spike-in proteins. DIA data was then analyzed using default settings and exported using the built in MSstats Report (v3.7.3) export schema. Quantification result is the same as in RMSV000000252.2. 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/c5wt7h
title: MassIVE Reanalysis RMSV000000258.7 - MassIVE.Quant-Reanalysis-Spectronaut-top10 features
title: A spectral library was generated using all available raw files (24 DDA files plus 24 DIA files) using the Pulsar search engine integrated in Spectronaut 11(11.0.15038) with default settings. Data processing was performed as described in the original manuscript. The uniprot human reference proteome from 2017.06.14 was used for the spectrum centric data analysis for library generation. Further included were the custom FASTA file for the spike-in proteins as well as the MaxQuant contaminants FASTA file. The resulting library was further filtered to remove all overlapping peptide sequences between the human background proteome and the spike-in proteins. DIA data was then analyzed using default settings and exported using the built in MSstats Report (v3.7.3) export schema. Quantification result is the same as in RMSV000000252.2. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5xt7t
title: MassIVE Reanalysis RMSV000000257.15 - MassIVE.Quant-Reanalysis-OpenSWATH-top10 features
title: Data processing was performed as described in the original manuscript, Navarro et al., 2016. The outputs for fragment-level quantification were used in further analysis. Quantification result is the same as in RMSV000000250.4. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c50m94
title: MassIVE Reanalysis RMSV000000259.2 - MassIVE.Quant-Reanalysis-Skyline-top5 features
title: Dataset was processed and quantified with Skyline (3.5.0.9319). Details for data processing are described in Choi, et al., 2017 and Panorama Web (https://panoramaweb.org/iPRG-2015.url) for iProphet cut-off 0.15. Quantification result is the same as in RMSV000000249.1. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c54b1k
title: MassIVE Reanalysis RMSV000000259.1 - MassIVE.Quant-Reanalysis-Skyline-top3 features
title: Dataset was processed and quantified with Skyline (3.5.0.9319). Details for data processing are described in Choi, et al., 2017 and Panorama Web (https://panoramaweb.org/iPRG-2015.url) for iProphet cut-off 0.15. Quantification result is the same as in RMSV000000249.1. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5843h
title: MassIVE Reanalysis RMSV000000258.12 - MassIVE.Quant-Reanalysis-DIAUmpire-feature selection
title: The raw files were converted to mzXML files with centroiding. The resulting mzXML files were processed by the signal extraction (SE) module of DIA-Umpire to generate pseudo-MSMS spectra. The generated pseudo-MS/MS spectra were searched using X! Tandem, Comet and MSGF+ search engines. The output files from the search engines were further analyzed by PeptideProphet and combined by iProphet. FDR filtering was done with PeptideProphet and ProteinProphet. DIA-Umpire's Quant module was for the quantification analysis. The outputs for all-level quantification (FragSummary, PeptideSummary, ProtSummary) were used in further analysis. Quantification result is the same as in RMSV000000252.3. 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/c5ct7v
title: MassIVE Reanalysis RMSV000000258.11 - MassIVE.Quant-Reanalysis-DIAUmpire-top10 features
title: The raw files were converted to mzXML files with centroiding. The resulting mzXML files were processed by the signal extraction (SE) module of DIA-Umpire to generate pseudo-MSMS spectra. The generated pseudo-MS/MS spectra were searched using X! Tandem, Comet and MSGF+ search engines. The output files from the search engines were further analyzed by PeptideProphet and combined by iProphet. FDR filtering was done with PeptideProphet and ProteinProphet. DIA-Umpire's Quant module was for the quantification analysis. The outputs for all-level quantification (FragSummary, PeptideSummary, ProtSummary) were used in further analysis. Quantification result is the same as in RMSV000000252.3. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5hh9r
title: MassIVE Reanalysis RMSV000000258.10 - MassIVE.Quant-Reanalysis-DIAUmpire-top5 features
title: The raw files were converted to mzXML files with centroiding. The resulting mzXML files were processed by the signal extraction (SE) module of DIA-Umpire to generate pseudo-MSMS spectra. The generated pseudo-MS/MS spectra were searched using X! Tandem, Comet and MSGF+ search engines. The output files from the search engines were further analyzed by PeptideProphet and combined by iProphet. FDR filtering was done with PeptideProphet and ProteinProphet. DIA-Umpire's Quant module was for the quantification analysis. The outputs for all-level quantification (FragSummary, PeptideSummary, ProtSummary) were used in further analysis. Quantification result is the same as in RMSV000000252.3. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5r42g
title: MassIVE Reanalysis RMSV000000259.4 - MassIVE.Quant-Reanalysis-Skyline-feature selection
title: Dataset was processed and quantified with Skyline (3.5.0.9319). Details for data processing are described in Choi, et al., 2017 and Panorama Web (https://panoramaweb.org/iPRG-2015.url) for iProphet cut-off 0.15. Quantification result is the same as in RMSV000000249.1. 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/c5vt76
title: MassIVE Reanalysis RMSV000000259.3 - MassIVE.Quant-Reanalysis-Skyline-top10 features
title: Dataset was processed and quantified with Skyline (3.5.0.9319). Details for data processing are described in Choi, et al., 2017 and Panorama Web (https://panoramaweb.org/iPRG-2015.url) for iProphet cut-off 0.15. Quantification result is the same as in RMSV000000249.1. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c53b18
title: MassIVE Reanalysis RMSV000000259.9 - MassIVE.Quant-Reanalysis-Progenesis-top3 features
title: Peptide features were identified with the Progenesis algorithm (v4.0.6403), aligned across all files, and annotated with the peptide identification resulting from the database search result from Comet. Quantification result is the same as in RMSV000000249.3. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c57436
title: MassIVE Reanalysis RMSV000000259.8 - MassIVE.Quant-Reanalysis-MaxQuant-feature selection
title: Dataset was processed and quantified with MaxQuant (v1.5.1.2) and Andromeda as a search engine. Quantification result is the same as in RMSV000000249.2. 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/c5bt7j
title: MassIVE Reanalysis RMSV000000259.7 - MassIVE.Quant-Reanalysis-MaxQuant-top10 features
title: Dataset was processed and quantified with MaxQuant (v1.5.1.2) and Andromeda as a search engine. Quantification result is the same as in RMSV000000249.2. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5fm95
title: MassIVE Reanalysis RMSV000000261.2 - MassIVE.Quant-Reanalysis-MaxQuant
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.
DOI: 10.25345/c5gm9g
title: MassIVE Reanalysis RMSV000000259.6 - MassIVE.Quant-Reanalysis-MaxQuant-top5 features
title: Dataset was processed and quantified with MaxQuant (v1.5.1.2) and Andromeda as a search engine. Quantification result is the same as in RMSV000000249.2. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5mb1x
title: MassIVE Reanalysis RMSV000000259.5 - MassIVE.Quant-Reanalysis-MaxQuant-top3 features
title: Dataset was processed and quantified with MaxQuant (v1.5.1.2) and Andromeda as a search engine. Quantification result is the same as in RMSV000000249.2. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5q43j
title: MassIVE Reanalysis RMSV000000259.12 - MassIVE.Quant-Reanalysis-Progenesis-feature selection
title: Peptide features were identified with the Progenesis algorithm (v4.0.6403), aligned across all files, and annotated with the peptide identification resulting from the database search result from Comet. Quantification result is the same as in RMSV000000249.3. 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/c5tt7w
title: MassIVE Reanalysis RMSV000000259.11 - MassIVE.Quant-Reanalysis-Progenesis-top10 features
title: Peptide features were identified with the Progenesis algorithm (v4.0.6403), aligned across all files, and annotated with the peptide identification resulting from the database search result from Comet. Quantification result is the same as in RMSV000000249.3. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5zm8f
title: MassIVE Reanalysis RMSV000000259.10 - MassIVE.Quant-Reanalysis-Progenesis-top5 features
title: Peptide features were identified with the Progenesis algorithm (v4.0.6403), aligned across all files, and annotated with the peptide identification resulting from the database search result from Comet. Quantification result is the same as in RMSV000000249.3. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c52f10
title: MassIVE Reanalysis RMSV000000261.6 - Reanalysis of MSV000084181 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000084181 - MassIVE.quant MSGF+
DOI: 10.25345/c5643w
title: MassIVE Reanalysis RMSV000000261.4 - MassIVE.Quant-Reanalysis-Proteome Discoverer
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.
DOI: 10.25345/c59t6v
title: MassIVE Reanalysis RMSV000000261.3 - MassIVE.Quant-Reanalysis-Progenesis
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.
DOI: 10.25345/c5dm9v
title: MassIVE Reanalysis RMSV000000262.5 - MassIVE.Quant-Reanalysis-Skyline-Full-50pct-all 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. 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/c5jf1b
title: MassIVE Reanalysis RMSV000000262.4 - MassIVE.Quant-Reanalysis-Skyline-Full-Sparse-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. 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/c5kb1m
title: MassIVE Reanalysis RMSV000000261.1 - MassIVE.Quant-Reanalysis-Skyline
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.