cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5tt6h
title: MassIVE Reanalysis RMSV000000222.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000080688 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c5zh9s
title: MassIVE Reanalysis RMSV000000221.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000080736 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c52b0k
title: MassIVE Reanalysis RMSV000000228.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000080842 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c5613v
title: MassIVE Reanalysis RMSV000000227.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000080749 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c59t5g
title: MassIVE Reanalysis RMSV000000226.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000080754 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c5fh94
title: MassIVE Reanalysis RMSV000000225.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000080695 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c5jb0x
title: MassIVE Reanalysis RMSV000000232.6 - CCMS Maestro reanalysis of CPTAC patient TCGA-AA-3518-01A-11
title: CCMS Maestro reanalysis of CPTAC colorectal cancer patient TCGA-AA-3518-01A-11 from dataset MSV000079852 / PXD014834
DOI: 10.25345/c5p136
title: MassIVE Reanalysis RMSV000000231.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000080816 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c5st66
title: MassIVE Reanalysis RMSV000000230.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000080694 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c5xh83
title: MassIVE Reanalysis RMSV000000229.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000080709 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c51b1n
title: MassIVE Reanalysis RMSV000000237.2 - MSGF+ 1% FDR - 50 ppm precursor mass tolerance
title: Automated MSGF-PLUS-AMBIGUITY reanalysis of dataset MSV000081649 at 1% FDR with 50 ppm precursor mass tolerance.
DOI: 10.25345/c5514x
title: MassIVE Reanalysis RMSV000000237.1 - MSGF+ Search for HCD Library
title: MSGF+ Search for MassIVE-KB HCD Human Library Creation
DOI: 10.25345/c58t6j
title: MassIVE Reanalysis RMSV000000235.3 - Test Reanalysis Attachment
title: This is a test reanalysis attachment. It is not real and is being attached only as a test of the reanalysis attachment workflow functionality.
DOI: 10.25345/c5dh8f
title: MassIVE Reanalysis RMSV000000235.2 - Test Reanalysis Attachment - MODa
title: This is a test of the reanalysis attachment workflow. These are some more words to satisfy the arbitrary minimum description length requirement.
DOI: 10.25345/c5hb10
title: MassIVE Reanalysis RMSV000000240.1 - MassIVE reanalysis test
title: test test test test test test test test test test test
DOI: 10.25345/c5n42j
title: MassIVE Reanalysis RMSV000000239.2 - Testing reanalysis with metadata files [1]
title: This is a test of the reanalysis attachment workflow. With files added to the "Metadata" collection, attachment should work with the summary file correctly showing all the files that were included.
DOI: 10.25345/c5rt5h
title: MassIVE Reanalysis RMSV000000239.1 - MSV000079843 Skyline reanalysis, result set 1 - "reanlz-01-Skyline-15cut-nosingle"
title: This is a test of new features related to reanalysis container privacy.
DOI: 10.25345/c5wm7f
title: MassIVE Reanalysis RMSV000000238.1 - Testing reanalysis attachments [1]
title: This is a test of reanalysis attachment workflow functionality.
DOI: 10.25345/c50b0z
title: MassIVE Reanalysis RMSV000000243.1 - Example MSGF+ reanalysis for CSE190 Fall 2018
title: Example reanalysis for CSE190 Fall 2018: MSGF+ search of profile analysis of NCI60 Leukemia cell line
DOI: 10.25345/c5442w
title: MassIVE Reanalysis RMSV000000242.1 - Example MSGF+ reanalyses for CSE190 Fall 2018
title: Example reanalyses for CSE190 Fall 2018: MSGF+ searches of deep analysis of NCI60 Leukemia and Ovarian cancer cell lines
DOI: 10.25345/c57t5v
title: MassIVE Reanalysis RMSV000000241.1 - Example MSPLIT-DIA reanalysis of Human 500ng using SwathAtlas
title: Example MSPLIT-DIA reanalysis of Human 500ng using SwathAtlas
DOI: 10.25345/c5cm7s
title: MassIVE Reanalysis RMSV000000240.2 - Reanalysis by MQ 1.6 test-2
title: Reanalysis by MaxQuant v1.6 and upload missing file and remove unused fasta file.
DOI: 10.25345/c5gb1p
title: MassIVE Reanalysis RMSV000000247.1 - CSE 190 Maestro Attachment
title: Non-small cell lung adenocarcinoma is the most frequently diagnosed lung cancer type and remains the leading cause of cancer mortality for men and women in the United States. Management of lung cancer is hindered by high false-positive rates due to the inability to resolve benign versus malignant tumors. Therefore, better molecular analysis comparing malignant and non-malignant tissues will provide additional evidence of the underlying biology contributing to tumorigenesis. In the current study, we utilized a proteomics approach to analyze 38 malignant and non-malignant paired tissue samples obtained from current or former smokers with early stage (Stage IA/IB) lung adenocarcinoma. Statistical mixed effects modeling and orthogonal partial least squares discriminant analysis were used to identify key cancer-associated perturbations in the malignant tissue proteome. Identified proteins were subsequently assessed against clinicopathological variables. [dataset license: CC0 1.0 Universal (CC0 1.0)] Maestro reanalysis
DOI: 10.25345/c5m43m
title: MassIVE Reanalysis RMSV000000246.1 - CSE190 Reanalysis: MSV000082948
title: Background MAP kinase inhibitor (MAPKi) therapy for BRAF mutated melanoma is characterized by high response rates but also development of drug resistance within a median progression-free survival (PFS) of 9 to 12 months. Understanding mechanisms of resistance and identifying effective therapeutic alternatives is one of the most important scientific challenges in melanoma. Using proteomics, we want to specifically gain insight into the pathophysiological process of cerebral metastases. Methods Cerebral metastases from melanoma patients were prepared for MS analysis by tryptic digestion. Mass spectrometric analysis was performed on a QExactive HF hybrid quadrupole-orbitrap mass spectrometer, equipped with a nanospray ion source, coupled with a nano HPLC system. Results In this pilot study, we were able to identify 5,977 proteins by LC-MS analysis. Samples were classified into good and poor responders based on PFS. By evaluating these proteomic profiles according to gene ontology (GO) terms, KEGG pathways and gene set enrichment analysis (GSEA), we could characterize differences between the two distinct groups. We further detected an EMT signature, V-type proton ATPases, calcium ion binding proteins, eukaryotic translation initiation factors, cell adhesion proteins and several transporter and exchanger proteins to be significantly up-regulated in poor responding patients, whereas good responders showed an immune-activation and involvement of extracellular matrix structural constituents, among other features. Subsequently we identified the most class-discriminating proteins based on nearest shrunken centroids. Conclusions Using proteomics helped to identify already known extra-cerebral resistance mechanisms in the cerebral metastases and further discovered possible brain specific mechanisms of drug efflux, which might serve as interesting targets, especially for treatment of these types of metastases or as predictive marker. [dataset license: CC0 1.0 Universal (CC0 1.0)] Maestro analysis
DOI: 10.25345/c5qt56
title: MassIVE Reanalysis RMSV000000245.1 - CSE190 Maestro Reanalysis: MSV000079972
title: We analyzed 84 tumor/normal pairs (177 total) using standard shotgun proteomic techniques in order to characterize the molecular landscape of clear cell renal cell carcinoma (ccRCC) and interrogated changes in protein abundance and biological pathways with ccRCC grade. These tissues were distributed across stage 1 (n = 34), 2 (n = 40), 3 (n = 42), and 4 (n = 52), with 9 pairs also including samples from metastasized tumor. These data can be (and were) combined with a previously published transcriptomic data set from the same sample cohort (NCBI GEO: GSE53757). [dataset license: CC0 1.0 Universal (CC0 1.0)] Maestro reanalysis
DOI: 10.25345/c5vm8h
title: MassIVE Reanalysis RMSV000000244.1 - CSE 190 Reanalysis
title: Maestro search of: The project analyzed 88 breast cancer clinical samples, including lymph node negative and positive primary tumors, lymph node metastases, and healthy tissue as control. All samples were combined with a super-SILAC mix that served as an internal standard for quantification. [dataset license: CC0 1.0 Universal (CC0 1.0)]
DOI: 10.25345/c5343z
title: MassIVE Reanalysis RMSV000000248.3 - MaxQuant reanalysis
title: MSV000079843 MaxQuant reanalysis
DOI: 10.25345/c56t6x
title: MassIVE Reanalysis RMSV000000248.2 - Skyline reanalysis
title: MSV000079843 Skyline reanalysis
DOI: 10.25345/c59m75
title: MassIVE Reanalysis RMSV000000248.11 - May Institute 2019 MassIVE.quant iPRG
title: Reanalysis using MaxQuant and Msstats of iPRG 2015 results.
DOI: 10.25345/c5bm7g
title: MassIVE Reanalysis RMSV000000248.1 - Maestro reanalysis a5416154cb034d72b9cb30c6f21c1a11
title: Maestro reanalysis for CCMS training activities. Original job URL https://proteomics.ucsd.edu/ProteoSAFe/status.jsp?task=a5416154cb034d72b9cb30c6f21c1a11
DOI: 10.25345/c5fd93
title: MassIVE Reanalysis RMSV000000248.10 - Msstats reanalysis training May Institute
title: Reanalyzed iPRG dataset during May Institute training using msstats
DOI: 10.25345/c5k439
title: MassIVE Reanalysis RMSV000000248.9 - MaxQuant (Maestro+ModDecode IDs) Reanalysis
title: MaxQuant Reanalysis using Maestro IDs. MSstats used too.
DOI: 10.25345/c5px4j
title: MassIVE Reanalysis RMSV000000248.8 - MaxQuant (MSGF+ IDs) Reanalysis
title: Reanalysis of iPRG dataset MaxQuant, run without a database. Using MSGF+ IDs and MSstats.
DOI: 10.25345/c5tm7t
title: MassIVE Reanalysis RMSV000000248.7 - MaxQuant (v1.6) reanalysis
title: MaxQuant Reanalysis of the iPRG Dataset. Andromeda IDs are used as well as MSstats.
DOI: 10.25345/c5zd9r
title: MassIVE Reanalysis RMSV000000248.4 - ProGenesis reanalysis
title: MSV000079843 ProGenesis reanalysis
DOI: 10.25345/c5243n
title: MassIVE Reanalysis RMSV000000248.13 - MassIVE.quant.iPRG_MayInstituteTraining
title: May Institute Training - iprg2015 working dataset.
DOI: 10.25345/c54x6b
title: MassIVE Reanalysis RMSV000000248.20 - MaxQuant (v 1.6) Reanalysis PS
title: Reanalysis of the iPRG dataset using MaxQuant and MS Stats offline.
DOI: 10.25345/c55x58
title: MassIVE Reanalysis RMSV000000248.12 - iPRG reanalysis using MaxQuant
title: reanalysis of iPRG2015 data using MaxQuant analysis and MSstats
DOI: 10.25345/c58m7v
title: MassIVE Reanalysis RMSV000000248.19 - LLP iPRG re analysis MsStats xxxxxxxxxxxxx
title: LLP iPRG re analysis MsStatsxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
DOI: 10.25345/c5dd9s
title: MassIVE Reanalysis RMSV000000248.18 - Reanalyis Data Set 2019 May Institute Training session
title: tutorial or reanalysis during P6 class for MassIVE
DOI: 10.25345/c5j430
title: MassIVE Reanalysis RMSV000000248.17 - MassIVE.quant iPRG reanalysis May Institute Introduction
title: This is a test to see how the MassIVE upload works and what parameters we need to fill out when doing a re-analysis.
DOI: 10.25345/c5nx5m
title: MassIVE Reanalysis RMSV000000248.16 - reanalysis_FV_maxquantiprgdataset
title: Reanalysis of iprg dataset using maxquant. No PTMs included in the search
DOI: 10.25345/c5sm7h
title: MassIVE Reanalysis RMSV000000248.15 - BJC_iprgMaxquant_20190509_Mayinstitute training
title: MASSive training - maxQuant reanalysis of iprg. blah blah blah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah lblah blah l
DOI: 10.25345/c5xf0c
title: MassIVE Reanalysis RMSV000000248.14 - ReAnalysis of iPRG for the MassIVE workshop
title: ReAnalysis of iPRG for the MassIVE workshop at the May Institute course in 2019 at the Northeastern university
DOI: 10.25345/c5072p
title: MassIVE Reanalysis RMSV000000248.33 - test-MSstats workflow-v1.1-maxquant-quant
title: test-MSstats workflow-v1.1-maxquant-quant-xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
DOI: 10.25345/c51720
title: MassIVE Reanalysis RMSV000000248.21 - Test reanalysis iPRG SR 8May19
title: Reanalysis of iPRG data - SR 8 May 2019 - to upload.
DOI: 10.25345/c57q8z
title: MassIVE Reanalysis RMSV000000248.29 - MassIVE.quant reanalysis from offline MaxQuant+MSstats results
title: &lt;a href="https://massive.ucsd.edu/ProteoSAFe/static/massive-quant.jsp"&gt;MassIVE.quant&lt;/a&gt; reanalysis of data from the iPRG2015 study (dataset &lt;a href="https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=eccf4bd3e86a4f79af468b0010eb80b0"&gt;MSV000079843&lt;/a&gt;) using Andromeda for identification and MaxQuant for quantification, followed by MSstats for statistical analysis of differentially abundant proteins.
DOI: 10.25345/c5cf0d
title: MassIVE Reanalysis RMSV000000248.26 - test add reanalysis for quantification by Meena version 2019.12.12
title: test add reanalysis for quantification by Meena version 1.2.9, 2019.12.12
DOI: 10.25345/c5h72b
title: MassIVE Reanalysis RMSV000000248.25 - iPRG data reanalysis by AMFN____________________________________________________________________________
DOI: 10.25345/c5mx59
title: MassIVE Reanalysis RMSV000000248.24 - BJC reanalysis of iprg with MaxQ
title: Re-analysis of iprg data with maxquant via MASSIVE on 20190508 during may institute training ..................................................................
DOI: 10.25345/c5rq8m
title: MassIVE Reanalysis RMSV000000248.23 - MayInstitute 2019 MassIVE Quant
title: dataset re-analyzed during MayInstitute MassIVE tutorial 2019, quantification by MaxQuant, statistical analysis by MSStats
DOI: 10.25345/c5wf02
title: MassIVE Reanalysis RMSV000000248.22 - May Institute 2019 MassIVE.quant iPRG
title: Reanalysis using MaxQuant and Msstats of iPRG 2015 results.
DOI: 10.25345/c53149
title: MassIVE Reanalysis RMSV000000249.3 - 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.
DOI: 10.25345/c53x61
title: MassIVE Reanalysis RMSV000000248.30 - MassIVE.quant reanalysis from offline MaxQuant results + online MSstats workflow results
title: &lt;a href="https://massive.ucsd.edu/ProteoSAFe/static/massive-quant.jsp"&gt;MassIVE.quant&lt;/a&gt; reanalysis of data from the iPRG2015 study (dataset &lt;a href="https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=eccf4bd3e86a4f79af468b0010eb80b0"&gt;MSV000079843&lt;/a&gt;) using Andromeda for identification and MaxQuant for quantification, followed by online analysis with MassIVE.quant's &lt;a href="https://massive.ucsd.edu/ProteoSAFe/index.jsp?params={%22workflow%22:%22MSSTATS%22}"&gt;online MSstats workflow&lt;/a&gt; for statistical analysis of differentially abundant proteins.
DOI: 10.25345/c56q8n
title: MassIVE Reanalysis RMSV000000249.2 - MassIVE.Quant-Reanalysis-MaxQuant
title: Dataset was processed and quantified with MaxQuant (v1.5.1.2) and Andromeda as a search engine.
DOI: 10.25345/c5bf03
title: MassIVE Reanalysis RMSV000000249.1 - MassIVE.Quant-Reanalysis-Skyline
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.
DOI: 10.25345/c5g721
title: MassIVE Reanalysis RMSV000000248.37 - MassIVE.quant reanalysis from MaxQuant (quant RMSV00000000249.2)+MSstats workflow v1.3
title: MassIVE.quant reanalysis of data from the iPRG2015 study (dataset MSV000079843) using Andromeda for identification and MaxQuant for quantification(from RMSV000000249.2), followed by MSstats for statistical analysis of differentially abundant proteins. Here MSstats(1.3) workflow was used.
DOI: 10.25345/c5kx6c
title: MassIVE Reanalysis RMSV000000248.36 - MassIVE.quant reanalysis from MaxQuant+MSstats workflow v1.3
title: MassIVE.quant reanalysis of data from the iPRG2015 study (dataset MSV000079843) using Andromeda for identification and MaxQuant for quantification, followed by MSstats for statistical analysis of differentially abundant proteins. Here MSstats(1.3) workflow was used.
DOI: 10.25345/c5qq89
title: MassIVE Reanalysis RMSV000000248.35 - MassIVE.quant reanalysis from offline MaxQuant+MSstats results
title: MassIVE.quant reanalysis of data from the iPRG2015 study (dataset MSV000079843) using Andromeda for identification and MaxQuant for quantification, followed by MSstats for statistical analysis of differentially abundant proteins.
DOI: 10.25345/c5vd9t
title: MassIVE Reanalysis RMSV000000248.34 - MassIVE.quant reanalysis from MaxQuant+ MSstats workflow from RMSV000000249.2
title: MassIVE.quant reanalysis of data from the iPRG2015 study (dataset MSV000079843) using Andromeda for identification and MaxQuant for quantification(from RMSV000000249.2), followed by MSstats for statistical analysis of differentially abundant proteins. Here MSstats(1.3) workflow was used.
DOI: 10.25345/c5z72c
title: MassIVE Reanalysis RMSV000000249.4 - MassIVE.Quant-Reanalysis-Skyline-iPhophetcut0.05
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, including proteins with a single peptide hit.
DOI: 10.25345/c52140
title: MassIVE Reanalysis RMSV000000249.15 - MassIVE.quant - MSGF+ Identifications
title: MSGF+ identifications for the IPRG2015 study for use in MassIVE.quant
DOI: 10.25345/c55q8b
title: MassIVE Reanalysis RMSV000000249.10 - MassIVE.Quant-Reanalysis-Skyline-iPhophetcut0.95-nosingle
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 0.95, excluding proteins with a single peptide hit.
DOI: 10.25345/c59j0t
title: MassIVE Reanalysis RMSV000000249.9 - MassIVE.Quant-Reanalysis-Skyline-iPhophetcut0.95
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 0.95, including proteins with a single peptide hit.
DOI: 10.25345/c5f72q
title: MassIVE Reanalysis RMSV000000249.8 - MassIVE.Quant-Reanalysis-Skyline-iPhophetcut0.50-nosingle
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 0.50, excluding proteins with a single peptide hit.
DOI: 10.25345/c5k138
title: MassIVE Reanalysis RMSV000000249.7 - MassIVE.Quant-Reanalysis-Skyline-iPhophetcut0.50
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 0.50, including proteins with a single peptide hit.
DOI: 10.25345/c5pq80
title: MassIVE Reanalysis RMSV000000249.6 - MassIVE.Quant-Reanalysis-Skyline-iPhophetcut0.15
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, including proteins with a single peptide hit.
DOI: 10.25345/c5sj05
title: MassIVE Reanalysis RMSV000000249.18 - MaxQuant 1.6.2.6 workflow, online MSstats workflow, comparison to RMSV000000249.2, id+quant mzTab
title: MassIVE.quant feature-complete submission with MaxQuant 1.6.2.6 run on ProteoSAFe, online MSstats workflow, a comparison to RMSV000000249.2 (MaxQuant 1.5 and offline MSstats), and a mzTab with both id and quant. Please note that in order to view the analyte abundances in the mzTab file you will need to download the file by (1) clicking the "FTP Download" button on the right, (2) opening the "result" folder and (3) saving the mzTab file. Alternatively you can also download the same mzTab file by (a) clicking on the "Browse Results" button on the right, (b) clicking "Download" tab at the top of the table and (c) clicking the "Download" button in the popup panel (the mzTab file will be in the "result" folder inside the zip file).
DOI: 10.25345/c5tj0g
title: MassIVE Reanalysis RMSV000000249.5 - MassIVE.Quant-Reanalysis-Skyline-iPhophetcut0.05-nosingle
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, excluding proteins with a single peptide hit.
DOI: 10.25345/c5x722
title: MassIVE Reanalysis RMSV000000249.16 - CCMS Reanalysis MassIVE.quant MaxQuant and online MSstats
title: Rerunning RMSV000000248.29 using online MSstats workflow, including comparison to RMSV000000248.29.
DOI: 10.25345/c5114p
title: MassIVE Reanalysis RMSV000000251.2 - MassIVE.Quant-Reanalysis-Skyline-All-nodup
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). Details for next steps are available in description.pdf
DOI: 10.25345/c54q7n
title: MassIVE Reanalysis RMSV000000251.1 - MassIVE.Quant-Reanalysis-Skyline-lowCV
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). Details for next steps are available in description.pdf
DOI: 10.25345/c58j0h
title: MassIVE Reanalysis RMSV000000250.4 - MassIVE.Quant-Reanalysis-OpenSWATH
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.
DOI: 10.25345/c5d72d
title: MassIVE Reanalysis RMSV000000250.3 - MassIVE.Quant-Reanalysis-DIAUmpire
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.
DOI: 10.25345/c5j14b
title: MassIVE Reanalysis RMSV000000250.2 - MassIVE.Quant-Reanalysis-Spectronaut
title: Data was reanalyzed in Spectronaut 11 (11.0.15038) using default settings and the library from the original manuscript, Navarro et al., 2016.