cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5mt6n
title: MassIVE Reanalysis RMSV000000252.1 - MassIVE.Quant-Reanalysis-Skyline
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. Details for next steps are available in description.pdf
DOI: 10.25345/c5nq8p
title: MassIVE Reanalysis RMSV000000250.1 - MassIVE.Quant-Reanalysis-Skyline
title: Data processing was performed with Skyline (3.1.1.8669) as described in the original manuscript for TripleTOF 6600, Iteration 2, Navarro et al., 2016.
DOI: 10.25345/c5rj0v
title: MassIVE Reanalysis RMSV000000251.4 - MassIVE.Quant-Reanalysis-DIAUmpire
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.
DOI: 10.25345/c5wb2s
title: MassIVE Reanalysis RMSV000000251.3 - MassIVE.Quant-Reanalysis-Spectronaut
title: A spectral library was generated using all available raw files from the original publication using the Pulsar search engine integrated in Spectronaut 11(11.0.15038) with default settings. The uniprot yeast reference proteome was used for the spectrum centric data analysis for library generation. DIA data was then analyzed using default settings and exported using the built in MSstats Report (v3.7.3) export schema.
DOI: 10.25345/c5014c
title: MassIVE Reanalysis RMSV000000255.1 - MassIVE.Quant-Reanalysis-MaxQuant
title: MS/MS spectra were searched using MaxQuant (v1.5.1.2) and Andromeda as search engine. Acquired data were searched against an UPS database containing all the spiked-in proteins, and the E. coli SwissProt protein database (November 2015 version). Details are available in the description file.
DOI: 10.25345/c53t60
title: MassIVE Reanalysis RMSV000000253.2 - MassIVE.Quant-Reanalysis-OpenSWATH
title: Details are described in Rost, et al., 2014. The supplementary data from Rost, et al., 2014 was used for further analysis.
DOI: 10.25345/c57j06
title: MassIVE Reanalysis RMSV000000253.1 - MassIVE.Quant-Reanalysis-Skyline
title: In Skyline (daily version 3.5.2.9703) a new document was created with default settings, plus heavy Lysine and Arginine with 13C and 15N labeling, and chromatogram extraction was set to use TOF extraction at 40,000 resolving power applying to all MS/MS spectra within a 25-m/z precursor isolation range around the 32-target m/z values used and 10 minutes of predicted retention times using the iRT library. Details for next steps are available in description.pdf
DOI: 10.25345/c5cb24
title: MassIVE Reanalysis RMSV000000252.3 - MassIVE.Quant-Reanalysis-DIAUmpire
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.
DOI: 10.25345/c5h141
title: MassIVE Reanalysis RMSV000000252.2 - MassIVE.Quant-Reanalysis-Spectronaut
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.
DOI: 10.25345/c5kt6b
title: MassIVE Reanalysis RMSV000000255.7 - MassIVE.Quant-Reanalysis-Skyline
title: The 8 raw files beginning with 20130510_EXQ1_IgPa_QC_UPS (the Dynamic Range Benchmark Dataset) for PRIDE PXD000279 were downloaded. In Skyline-daily (version 3.5.1.9327), using the results (msms.txt) produced by MaxQuant (v1.5.0.0) with the Andromeda search engine, as described in Cox2014_DDA_MaxQuant_description.pdf in RMSV000000255.1(MassIVE Reanalysis ID), a spectral library was built with 0.99 cut-off score and ambiguous spectrum matches not included. A new document was created with default settings plus the new library, Oxidation (M), Acetyl (N-Term), Acetyl (S), and Acetyl (T), precursors charge states 2-4, ion type 'p' and chromatogram extraction of 3 isotope peaks was set to use 15 ppm mass tolerance applying to all centroided MS1 spectra within 5 minutes of MS/MS IDs. The 3 (human, E. coli, contaminants) proteome sequence (FASTA) files mentioned in the original paper methods were imported into the new document, with repeated peptides and empty proteins removed, resulting in 2,269 proteins, 20,091 peptides, and 25,920 precursors. The 8 runs were then imported into the template for chromatogram extraction, retention time alignment, and automatic peak picking. The MSstats report was exported for further analysis. The differential abundance analysis was performed by MSstats (v3.13.5) R package. description.pdf including details for data processing and statistical analysis and R script are available in the 'methods' folder.
DOI: 10.25345/c5qh9m
title: MassIVE Reanalysis RMSV000000255.6 - Reanalysis of MSV000081831 - MassIVE.quant MSGF+ Identifications
title: MassIVE.quant Identifications from Reanalysis of MSV000081831 - MassIVE.quant MSGF+
DOI: 10.25345/c5vb2g
title: MassIVE Reanalysis RMSV000000255.5 - CCMS Reanalysis of DDA, Cox: MaxQuant
title: MassIVE.quant online reanalysis of DDA, Cox: MaxQuant (MSV000081831 - RMSV000000255.1)
DOI: 10.25345/c52t6p
title: MassIVE Reanalysis RMSV000000256.3 - ProteoCarta reanalysis of Bifidobacterium longum infantis ATCC15697
title: ProteoCarta reanalysis of Bifidobacterium longum infantis ATCC15697
DOI: 10.25345/c55m89
title: MassIVE Reanalysis RMSV000000256.10 - ProteoCarta reanalysis of Campylobacter jejuni
title: ProteoCarta reanalysis of Campylobacter jejuni
DOI: 10.25345/c56h9z
title: MassIVE Reanalysis RMSV000000256.2 - ProteoCarta reanalysis of Coprococcus comes ATCC27758
title: ProteoCarta reanalysis of Coprococcus comes ATCC27758
DOI: 10.25345/c5bb2t
title: MassIVE Reanalysis RMSV000000256.1 - ProteoCarta reanalysis of Prevotella ruminicola 23 ATCC 19189
title: ProteoCarta reanalysis of Prevotella ruminicola 23 ATCC 19189
DOI: 10.25345/c5g14q
title: MassIVE Reanalysis RMSV000000255.8 - MassIVE.Quant-Reanalysis-Progenesis
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. Unique semi-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 (v3.13.5) R package. description.pdf including details for data processing and statistical analysis and R script are available in the 'methods' folder.
DOI: 10.25345/c5jt7d
title: MassIVE Reanalysis RMSV000000256.7 - ProteoCarta reanalysis of Pseudomonas putida KT2440
title: ProteoCarta reanalysis of Pseudomonas putida KT2440
DOI: 10.25345/c5pm8z
title: MassIVE Reanalysis RMSV000000256.6 - ProteoCarta reanalysis of Shewanella oneidensis MR-1
title: ProteoCarta reanalysis of Shewanella oneidensis MR-1
DOI: 10.25345/c5tb25
title: MassIVE Reanalysis RMSV000000256.5 - ProteoCarta reanalysis of Streptomyces venezuelae
title: ProteoCarta reanalysis of Streptomyces venezuelae
DOI: 10.25345/c5z443
title: MassIVE Reanalysis RMSV000000256.4 - ProteoCarta reanalysis of Bifidobacterium bifidum ATCC29521
title: ProteoCarta reanalysis of Bifidobacterium bifidum ATCC29521
DOI: 10.25345/c51t6c
title: MassIVE Reanalysis RMSV000000256.11 - ProteoCarta reanalysis of Sulfobacillus thermosulfidooxidans
title: ProteoCarta reanalysis of Sulfobacillus thermosulfidooxidans
DOI: 10.25345/c58b1t
title: MassIVE Reanalysis RMSV000000256.17 - ProteoCarta reanalysis of Rhodococcus jostii RHA1
title: ProteoCarta reanalysis of Rhodococcus jostii RHA1
DOI: 10.25345/c59b14
title: MassIVE Reanalysis RMSV000000256.9 - ProteoCarta reanalysis of Legionella pneumophila
title: ProteoCarta reanalysis of Legionella pneumophila
DOI: 10.25345/c5f432
title: MassIVE Reanalysis RMSV000000256.8 - ProteoCarta reanalysis of Methylomicrobium alcaliphilum
title: ProteoCarta reanalysis of Methylomicrobium alcaliphilum
DOI: 10.25345/c5ht6q
title: MassIVE Reanalysis RMSV000000256.15 - ProteoCarta reanalysis of Streptococcus agalactiae
title: ProteoCarta reanalysis of Streptococcus agalactiae
DOI: 10.25345/c5nm8n
title: MassIVE Reanalysis RMSV000000256.14 - ProteoCarta reanalysis of Stigmatella aurantiaca DW4_3-1
title: ProteoCarta reanalysis of Stigmatella aurantiaca DW4_3-1
DOI: 10.25345/c5sb1g
title: MassIVE Reanalysis RMSV000000256.13 - ProteoCarta reanalysis of Synechococcus elongatus PCC7942
title: ProteoCarta reanalysis of Synechococcus elongatus PCC7942
DOI: 10.25345/c5x44s
title: MassIVE Reanalysis RMSV000000256.12 - ProteoCarta reanalysis of Streptomyces griseorubens
title: ProteoCarta reanalysis of Streptomyces griseorubens
DOI: 10.25345/c50x5q
title: MassIVE Reanalysis RMSV000000256.19 - ProteoCarta reanalysis of Paenibacillus polymyxa ATCC842
title: ProteoCarta reanalysis of Paenibacillus polymyxa ATCC842
DOI: 10.25345/c53m8p
title: MassIVE Reanalysis RMSV000000256.26 - ProteoCarta reanalysis of Lactobacillus casei
title: ProteoCarta reanalysis of Lactobacillus casei
DOI: 10.25345/c54m9c
title: MassIVE Reanalysis RMSV000000256.18 - ProteoCarta reanalysis of Ruminococcus gnavus
title: ProteoCarta reanalysis of Ruminococcus gnavus
DOI: 10.25345/c5c43f
title: MassIVE Reanalysis RMSV000000256.24 - ProteoCarta reanalysis of Micrococcus luteus
title: ProteoCarta reanalysis of Micrococcus luteus
DOI: 10.25345/c5d444
title: MassIVE Reanalysis RMSV000000256.16 - ProteoCarta reanalysis of Rhodopseudomonas palustris
title: ProteoCarta reanalysis of Rhodopseudomonas palustris
DOI: 10.25345/c5gx52
title: MassIVE Reanalysis RMSV000000256.23 - ProteoCarta reanalysis of Mycobacterium smegmatis
title: ProteoCarta reanalysis of Mycobacterium smegmatis
DOI: 10.25345/c5mm9q
title: MassIVE Reanalysis RMSV000000256.22 - ProteoCarta reanalysis of Myxococcus xanthus
title: ProteoCarta reanalysis of Myxococcus xanthus
DOI: 10.25345/c5rf0t
title: MassIVE Reanalysis RMSV000000256.21 - ProteoCarta reanalysis of Paracoccus denitrificans
title: ProteoCarta reanalysis of Paracoccus denitrificans
DOI: 10.25345/c5w44g
title: MassIVE Reanalysis RMSV000000256.20 - ProteoCarta reanalysis of Anaerococcus hydrogenalis DSM 7454
title: ProteoCarta reanalysis of Anaerococcus hydrogenalis DSM 7454
DOI: 10.25345/c56f17
title: MassIVE Reanalysis RMSV000000256.33 - ProteoCarta reanalysis of Fibrobacter succinogenes S85
title: ProteoCarta reanalysis of Fibrobacter succinogenes S85
DOI: 10.25345/c57f05
title: MassIVE Reanalysis RMSV000000256.25 - ProteoCarta reanalysis of Listeria monocytogenes 10403S
title: ProteoCarta reanalysis of Listeria monocytogenes 10403S
DOI: 10.25345/c5b434
title: MassIVE Reanalysis RMSV000000256.32 - ProteoCarta reanalysis of Erythrobacter HL-111
title: ProteoCarta reanalysis of Erythrobacter HL-111
DOI: 10.25345/c5fx64
title: MassIVE Reanalysis RMSV000000256.31 - ProteoCarta reanalysis of Halomonas HL-48
title: ProteoCarta reanalysis of Halomonas HL-48
DOI: 10.25345/c5km81
title: MassIVE Reanalysis RMSV000000256.30 - ProteoCarta reanalysis of Algoriphagus marincola HL-49
title: ProteoCarta reanalysis of Algoriphagus marincola HL-49
DOI: 10.25345/c5qf1w
title: MassIVE Reanalysis RMSV000000256.29 - ProteoCarta reanalysis of Cyanobacterium stanieri
title: ProteoCarta reanalysis of Cyanobacterium stanieri
DOI: 10.25345/c5v43s
title: MassIVE Reanalysis RMSV000000256.28 - ProteoCarta reanalysis of Rhodobacteraceae bacterium HL-91
title: ProteoCarta reanalysis of Rhodobacteraceae bacterium HL-91
DOI: 10.25345/c5zx6s
title: MassIVE Reanalysis RMSV000000256.27 - ProteoCarta reanalysis of Halomonas HL-93
title: ProteoCarta reanalysis of Halomonas HL-93
DOI: 10.25345/c51q83
title: MassIVE Reanalysis RMSV000000256.42 - ProteoCarta reanalysis of Cellulomonas gilvus
title: ProteoCarta reanalysis of Cellulomonas gilvus
DOI: 10.25345/c52q71
title: MassIVE Reanalysis RMSV000000256.34 - ProteoCarta reanalysis of Faecalibacterium prausnitzii
title: ProteoCarta reanalysis of Faecalibacterium prausnitzii
DOI: 10.25345/c55f0j
title: MassIVE Reanalysis RMSV000000256.41 - ProteoCarta reanalysis of Citrobacter freundii
title: ProteoCarta reanalysis of Citrobacter freundii
DOI: 10.25345/c5973v
title: MassIVE Reanalysis RMSV000000256.40 - ProteoCarta reanalysis of Chryseobacterium indologenes
title: ProteoCarta reanalysis of Chryseobacterium indologenes
DOI: 10.25345/c5dx5f
title: MassIVE Reanalysis RMSV000000256.39 - ProteoCarta reanalysis of Clostridium ljungdahlii DSM 13528
title: ProteoCarta reanalysis of Clostridium ljungdahlii DSM 13528
DOI: 10.25345/c5jq7c
title: MassIVE Reanalysis RMSV000000256.38 - ProteoCarta reanalysis of Cupriavidus necator N-1
title: ProteoCarta reanalysis of Cupriavidus necator N-1
DOI: 10.25345/c5pf1k
title: MassIVE Reanalysis RMSV000000256.37 - ProteoCarta reanalysis of Delftia acidovorans
title: ProteoCarta reanalysis of Delftia acidovorans
DOI: 10.25345/c5t724
title: MassIVE Reanalysis RMSV000000256.36 - ProteoCarta reanalysis of Dorea longicatena
title: ProteoCarta reanalysis of Dorea longicatena
DOI: 10.25345/c5xx53
title: MassIVE Reanalysis RMSV000000256.35 - ProteoCarta reanalysis of Francisella novicida
title: ProteoCarta reanalysis of Francisella novicida
DOI: 10.25345/c50q7d
title: MassIVE Reanalysis RMSV000000256.50 - ProteoCarta reanalysis of Agrobacterium tumefaciens IAM 12048
title: ProteoCarta reanalysis of Agrobacterium tumefaciens IAM 12048
DOI: 10.25345/c54h9b
title: MassIVE Reanalysis RMSV000000256.49 - ProteoCarta reanalysis of Alcaligenes faecalis
title: ProteoCarta reanalysis of Alcaligenes faecalis
DOI: 10.25345/c5873j
title: MassIVE Reanalysis RMSV000000256.48 - ProteoCarta reanalysis of Bacillus subtilis 168
title: ProteoCarta reanalysis of Bacillus subtilis 168
DOI: 10.25345/c5cx4r
title: MassIVE Reanalysis RMSV000000256.47 - ProteoCarta reanalysis of Bacillus cereus ATCC14579
title: ProteoCarta reanalysis of Bacillus cereus ATCC14579
DOI: 10.25345/c5hq72
title: MassIVE Reanalysis RMSV000000256.46 - ProteoCarta reanalysis of Bacteroides fragilis 638R
title: ProteoCarta reanalysis of Bacteroides fragilis 638R
DOI: 10.25345/c5nf18
title: MassIVE Reanalysis RMSV000000256.45 - ProteoCarta reanalysis of Bacillus subtilis NCIB3610
title: ProteoCarta reanalysis of Bacillus subtilis NCIB3610
DOI: 10.25345/c5s736
title: MassIVE Reanalysis RMSV000000256.44 - ProteoCarta reanalysis of Bacteroides thetaiotaomicron VPI-5482
title: ProteoCarta reanalysis of Bacteroides thetaiotaomicron VPI-5482
DOI: 10.25345/c5wx5s
title: MassIVE Reanalysis RMSV000000256.43 - ProteoCarta reanalysis of Cellulophaga baltica 18
title: ProteoCarta reanalysis of Cellulophaga baltica 18
DOI: 10.25345/c53h91
title: MassIVE Reanalysis RMSV000000257.6 - MassIVE.Quant-Reanalysis-Spectronaut-top5 features
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. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c57737
title: MassIVE Reanalysis RMSV000000257.5 - MassIVE.Quant-Reanalysis-Spectronaut-top3 features
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. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5c155
title: MassIVE Reanalysis RMSV000000257.4 - MassIVE.Quant-Reanalysis-Skyline-feature selection
title: Data processing was performed with Skyline (3.1.1.8669) as described in the original manuscript for TripleTOF 6600, Iteration 2, Navarro et al., 2016. Quantification result is the same as in RMSV000000250.1. 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/c5gq7r
title: MassIVE Reanalysis RMSV000000257.3 - MassIVE.Quant-Reanalysis-Skyline-top10 features
title: Data processing was performed with Skyline (3.1.1.8669) as described in the original manuscript for TripleTOF 6600, Iteration 2, Navarro et al., 2016. Quantification result is the same as in RMSV000000250.1. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5mh9p
title: MassIVE Reanalysis RMSV000000257.2 - MassIVE.Quant-Reanalysis-Skyline-top5 features
title: Data processing was performed with Skyline (3.1.1.8669) as described in the original manuscript for TripleTOF 6600, Iteration 2, Navarro et al., 2016. Quantification result is the same as in RMSV000000250.1. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5r73w
title: MassIVE Reanalysis RMSV000000257.1 - MassIVE.Quant-Reanalysis-Skyline-top3 features
title: Data processing was performed with Skyline (3.1.1.8669) as described in the original manuscript for TripleTOF 6600, Iteration 2, Navarro et al., 2016. Top 3 features were used for statistical analysis in MSstats R package.
DOI: 10.25345/c5w14f
title: MassIVE Reanalysis RMSV000000256.51 - ProteoCarta reanalysis of Acidiphilium cryptum JF-5
title: ProteoCarta reanalysis of Acidiphilium cryptum JF-5
DOI: 10.25345/c5zq73
title: MassIVE Reanalysis RMSV000000257.7 - MassIVE.Quant-Reanalysis-Spectronaut-top10 features
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. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c52h9q
title: MassIVE Reanalysis RMSV000000257.14 - MassIVE.Quant-Reanalysis-OpenSWATH-top5 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 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c56b16
title: MassIVE Reanalysis RMSV000000257.13 - MassIVE.Quant-Reanalysis-OpenSWATH-top3 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 3 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5b15v
title: MassIVE Reanalysis RMSV000000257.12 - MassIVE.Quant-Reanalysis-DIAUmpire-feature selection
title: Data processing was performed as described in the original manuscript, Navarro et al., 2016. 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. Quantification result is the same as in RMSV000000250.3. 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/c5fq62
title: MassIVE Reanalysis RMSV000000257.11 - MassIVE.Quant-Reanalysis-DIAUmpire-top10 features
title: Data processing was performed as described in the original manuscript, Navarro et al., 2016. 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. Quantification result is the same as in RMSV000000250.3. Top 10 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5kh9c
title: MassIVE Reanalysis RMSV000000257.10 - MassIVE.Quant-Reanalysis-DIAUmpire-top5 features
title: Data processing was performed as described in the original manuscript, Navarro et al., 2016. 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. Quantification result is the same as in RMSV000000250.3. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
DOI: 10.25345/c5q73k
title: MassIVE Reanalysis RMSV000000257.9 - MassIVE.Quant-Reanalysis-DIAUmpire-top3 features
title: Data processing was performed as described in the original manuscript, Navarro et al., 2016. 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. Quantification result is the same as in RMSV000000250.3. Top 3 features were used for statistical analysis in MSstats R package for this reanalysis.