cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c56147
title: MassIVE Reanalysis RMSV000000263.12 - MassIVE.Quant-Reanalysis-Progenesis-feature selection
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. 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/c58q7w
title: MassIVE Reanalysis RMSV000000264.8 - 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 RMSV000000264.7. 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/c5dh9t
title: MassIVE Reanalysis RMSV000000264.7 - MassIVE.quant reanalysis from offline PD+MSstatsTMT results
title: MassIVE.quant reanalysis for MSstatsTMT for Mouse3mix_PD data from Plubell et al. The PSM files from Proteome Discoverer were exported to R to perform data preprocessing, multiple fractions combination, data normalization with reference channel, protein summarization and statistical testing using MSstatsTMT v1.6.2. R script for statistical analysis with MSstatsTMT is available (mouse3mix_PD_Rscript.R).
DOI: 10.25345/c5j72n
title: MassIVE Reanalysis RMSV000000264.6 - Reanalysis of MSV000082569 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000082569 - MassIVE.quant MSGF+
DOI: 10.25345/c5p14k
title: MassIVE Reanalysis RMSV000000263.16 - MassIVE.Quant-Reanalysis-ProteomeDiscoverer-feature selection
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. 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/c5sq8x
title: MassIVE Reanalysis RMSV000000263.15 - MassIVE.Quant-Reanalysis-ProteomeDiscoverer-top10 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 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5xh9g
title: MassIVE Reanalysis RMSV000000263.14 - MassIVE.Quant-Reanalysis-ProteomeDiscoverer-top5 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 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5173c
title: MassIVE Reanalysis RMSV000000264.10 - MassIVE.quant reanalysis from offline PD+Sum+IRS+edgeR 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 preprocessing, log(sum) protein summarization, IRS normalization, and statistical testing using edgeR v3.30.3. was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script are available in the 'methods' folder.
DOI: 10.25345/c5389m
title: MassIVE MSV000083204 - GNPS-shm-20181210
title: institute of medicinal biotechnology chinese academy of meical sciences, china
DOI: 10.25345/c5414m
title: MassIVE Reanalysis RMSV000000266.5 - MassIVE.quant reanalysis from offline PD+MSstatsTMT results
title: Raw data were processed using Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific) and Mascot Server 2.6.1 (Matrix Science, London). Processing workflows were designed to perform a two-pass search on the MS2 data. First, the data were searched against the UniProt/SwissProt human protein database (07.2018 release, 20398 entries) using trypsin/P as an enzyme, a maximum of two missed cleavage sites, and 10 ppm, as the precursor ion mass tolerance. 0.5 and 0.1 Da were specified as the fragment ion mass tolerances for MS3 and MS2, respectively. Carbamidomethylated cysteines (+57.02146 Da), TMT10 and SILAC K8 labeled lysines (+237.177131 Da), SILAC R10 arginines (+10.008269 Da), and TMT10 labeled peptide N-termini (+229.162932 Da) were set as static, while oxidized methionines (+15.99492 Da) were set as dynamic modifications. Second, the data were searched against the human protein database for which the endogenous sequence were replaced with UPS sequences (protein entries marked with ups, 20395 entries), using carbamidomethylated cysteines, TMT10 labeled lysines and peptide Ntermini as static, and oxidized methionines as dynamic modifications. The peptide-to-spectrum matches (PSMs) false discovery rates (FDRs) were controlled using Percolator and setting a max. delta Cn of 0.05 and a q-value threshold of 0.01. Reporter ion quantitation was performed using the MS2 data order, 3 mmu peak integration and most confident centroid tolerances. Reporter ion intensities were adjusted to correct for the isotopic impurities of the different TMT reagents (manufacturer specifications). Reporter ions intensities were used to express abundances. PSMs from all ranks were considered, peptide FDRs were controlled by setting a q-value threshold of 0.01 and allowing the software to automatically select PSM q-value or ion score for the grouping (PSM FDR was 0.89%, peptide group FDR was 1.21%). High confidence peptides with a minimal length of 6 residues were further grouped into proteins and protein FDR was set to fulfill a q-value threshold of 0.01. At this level, protein FDR was 1.09%. For protein grouping, strict parsimony principle was applied. The report for PSM level from Proteome Discoverer was used for downstream statistical analysis. For statistical analysis, data preprocessing, multiple fractions combination, data normalization with reference channel, protein summarization and statistical testing using MSstatsTMT v1.6.2 was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script are available in the methods folder.
DOI: 10.25345/c57012
title: MassIVE MSV000083203 - GNPS-herbicidin F1 and F5
title: Herbicidins are adenosine-based nucleoside
antibiotics with an unusual tricyclic undecose core
decorated with a (5-hydroxy)tiglyl moiety. Feeding studies
are herein reported demonstrating that the tricyclic core is
derived from D-glucose and D-ribose, whereas the tiglyl
moiety is derived from an intermediate of L-isoleucine
catabolism. Identification of the gene cluster for herbicidin
A biosynthesis in Streptomyces sp. L-9-10 as well as its
verification by heterologous expression in a nonproducing
host are described, and the results of in vitro characterization
of a carboxyl methyltransferase encoded in the
cluster, Her8, are presented. Based on these observations, a
biosynthetic pathway is proposed for herbicidins.
DOI: 10.25345/c57t67
title: MassIVE Reanalysis RMSV000000266.4 - Reanalysis of MSV000084266 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000084266 - MassIVE.quant MSGF+
DOI: 10.25345/c5bs42
title: MassIVE MSV000083201 - AJS-ESI analysis of the Spleen of Npc1 null mice
title: AJS-ESI LFQ analysis in spleen tissue from 11-week mutant and control and mutant mice
DOI: 10.25345/c5cj0f
title: MassIVE Reanalysis RMSV000000265.13 - MassIVE.quant reanalysis from offline PD+MSstatsTMT results
title: Raw data were processed using Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific) and Mascot Server 2.6.1 (Matrix Science, London). Processing workflows were designed to perform a two-pass search on the MS2 data. First, the data were searched against the UniProt/SwissProt human protein database (07.2018 release, 20398 entries) using trypsin/P as an enzyme, a maximum of two missed cleavage sites, and 10 ppm, as the precursor ion mass tolerance. 0.5 and 0.1 Da were specified as the fragment ion mass tolerances for MS3 and MS2, respectively. Carbamidomethylated cysteines (+57.02146 Da), TMT10 and SILAC K8 labeled lysines (+237.177131 Da), SILAC R10 arginines (+10.008269 Da), and TMT10 labeled peptide N-termini (+229.162932 Da) were set as static, while oxidized methionines (+15.99492 Da) were set as dynamic modifications. Second, the data were searched against the human protein database for which the endogenous sequence were replaced with UPS sequences (protein entries marked with ups, 20395 entries), using carbamidomethylated cysteines, TMT10 labeled lysines and peptide Ntermini as static, and oxidized methionines as dynamic modifications. The peptide-to-spectrum matches (PSMs) false discovery rates (FDRs) were controlled using Percolator and setting a max. delta Cn of 0.05 and a q-value threshold of 0.01. Reporter ion quantitation was performed using the MS3 data order (SPS-MS3 method), 3 mmu peak integration and most confident centroid tolerances. Reporter ion intensities were adjusted to correct for the isotopic impurities of the different TMT reagents (manufacturer specifications). Reporter ions intensities were used to express abundances. PSMs from all ranks were considered, peptide FDRs were controlled by setting a q-value threshold of 0.01 and allowing the software to automatically select PSM q-value or ion score for the grouping (PSM FDR was 0.89%, peptide group FDR was 1.21%). High confidence peptides with a minimal length of 6 residues were further grouped into proteins and protein FDR was set to fulfill a q-value threshold of 0.01. At this level, protein FDR was 1.09%. For protein grouping, strict parsimony principle was applied. The report for PSM level from Proteome Discoverer was used for downstream statistical analysis. For statistical analysis, data preprocessing, multiple fractions combination, data normalization with reference channel, protein summarization and statistical testing using MSstatsTMT v1.6.2 was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script are available in the methods folder.
DOI: 10.25345/c5h73q
title: MassIVE Reanalysis RMSV000000265.12 - MassIVE.quant reanalysis from offline PD+Sum+IRS+edgeR results
title: The same PSM report from Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific) in RMSV000000265.9 was used for this reanalysis. For statistical analysis, data preprocessing, log(sum) protein summarization, IRS normalization, and statistical testing using edgeR v3.30.3. was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script are available in the 'methods' folder.
DOI: 10.25345/c5k89z
title: MassIVE MSV000083210 - GNPS-shm20181201-1
title: institute of medicinal biotechnology chinese academy of meical sciences, china
DOI: 10.25345/c5n15n
title: MassIVE Reanalysis RMSV000000265.11 - 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 RMSV000000265.9 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/c5q01d
title: MassIVE MSV000083209 - GNPS Lignans
title: The uploaded folder contains the mzXML files of some raw spectrum files obtained from an LC-MS system. The overall goal of this submission is to find some lignans in 4 murine blood serum samples.
DOI: 10.25345/c5rq90
title: MassIVE Reanalysis RMSV000000265.10 - 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 RMSV000000265.9. 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/c5ts4d
title: MassIVE MSV000083206 - GNPS-shm20181210
title: institute of medicinal biotechnology chinese academy of meical sciences, china
DOI: 10.25345/c5wj03
title: MassIVE Reanalysis RMSV000000265.8 - Reanalysis of MSV000084264 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000084264 - MassIVE.quant MSGF+
DOI: 10.25345/c5zg69
title: MassIVE MSV000083205 - GNPS-shm-20181210
title: institute of medicinal biotechnology chinese academy of meical sciences, china
DOI: 10.25345/c50b1b
title: MassIVE Reanalysis RMSV000000266.6 - MassIVE.quant reanalysis from offline PD+Sum+IRS+edgeR 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 preprocessing, log(sum) protein summarization, IRS normalization, and statistical testing using edgeR v3.30.3. was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script are available in the 'methods' folder.
DOI: 10.25345/c5288x
title: MassIVE MSV000083215 - Celtis_occidentalis_leaf
title: n-butanol peptide extract of Celtis occidentalis leaves
DOI: 10.25345/c5315p
title: MassIVE Reanalysis RMSV000000267.12 - 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 same data processing step in Proteome Discoverer as in RMSV000000267.7 was performed. 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 result is available in the methods folder.
DOI: 10.25345/c56024
title: MassIVE MSV000083214 - Build 521 Multi-enzyme LFQuan of DSSO crosslinked MRN complex data
title: Build 521 Multi-enzyme LFQuan of DSSO crosslinked MRN complex data
DOI: 10.25345/c56t79
title: MassIVE Reanalysis RMSV000000267.10 - 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 RMSV000000267.7 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 are available in the 'methods' folder.
DOI: 10.25345/c59s3c
title: MassIVE MSV000083213 - GNPS-shm20181210-2
title: institute of medicinal biotechnology chinese academy of meical sciences, china
DOI: 10.25345/c5bj04
title: MassIVE Reanalysis RMSV000000267.9 - MassIVE.quant reanalysis from offline PD+Sum+IRS+edgeR results
title: The same PSM report from Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific) in RMSV000000267.7 was used for this reanalysis. For statistical analysis, data preprocessing, log(sum) protein summarization, IRS normalization and statistical testing using edgeR v3.30.3. was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script are available in the 'methods' folder.
DOI: 10.25345/c5fg71
title: MassIVE MSV000083212 - GNPS-sansanmycin
title: A new iridoid glycoside, named camptoside (1), together with three known compounds as dehydrodiconiferyl alcohol-glucopyranoside (2), aesculetin (3) and vajicoside (4), have been isolated from Camptosorus sibiricus Rupr for the first time.
DOI: 10.25345/c5gb22
title: MassIVE Reanalysis RMSV000000267.7 - MassIVE.quant reanalysis from offline PD+MSstatsTMT results
title: Raw data were processed using Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific) and Mascot Server 2.6.2 (Matrix Science, London). A processing workflow was designed to search the MS2 data against the UniProt/SwissProt S. cerevisiae protein database (strain S288c, 07.2017 release, 9,721 entries) using trypsin/P as an enzyme, a maximum of two missed cleavage sites, 10 ppm and 0.5 Da, as the precursor, and fragment ion mass tolerances, respectively. Carbamidomethylated cysteines (+57.02146 Da), TMT10 labeled lysines and peptide N-termini (+229.162932 Da) were set as static, while oxidized methionines (+15.99492 Da) were set as dynamic modifications. The peptide-to-spectrum matches (PSMs) false discovery rates (FDRs) were controlled using Percolator and setting a max. delta Cn of 0.05 and a q-Value threshold of 0.01 (strict). Reporter ion quantitation was performed using the MS3 data order, 3 mmu peak integration and most confident centroid tolerances. Reporter ion intensities were adjusted to correct for the isotopic impurities of the different TMT reagents (manufacturer specifications). Reporter ions intensities or signal to noise (S/N) ratio (2) were used to express abundances. A consensus workflow was defined to group PSMs into peptide and proteins. PSMs from all ranks were considered, peptide FDRs were controlled by setting a q-Value threshold of 0.01 and allowing the software to automatically select PSM q-Value or ion score for the grouping (PSM FDR was 1.0%, peptide group FDR was 1.8%). High confidence peptides with a minimal length of 6 residues were further grouped into proteins and protein FDR was set to fulfill a q-Value threshold of 0.01. At this level, protein FDR was 1.0%. For protein grouping, strict parsimony principle was applied. Peptide and protein quantitation was performed by summing intensities for each channel and normalizing each value with the highest TMT channel total. For protein quantitation, unique peptides only were considered. Finally, individual peptide and protein intensities were scaled to an average of 100. The report for PSM level from Proteome Discoverer was used for downstream statistical analysis. For statistical analysis, data preprocessing, multiple fractions combination, data normalization with reference channel, protein summarization and statistical testing using MSstatsTMT v1.6.2 was performed. description.pdf including details for data processing by Proteome Discoverer and statistical analysis and R script are available in the 'methods' folder.
DOI: 10.25345/c5m14z
title: MassIVE Reanalysis RMSV000000267.6 - Reanalysis of MSV000084263 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000084263 - MassIVE.quant MSGF+