Casanovo de novo peptide sequencing immunopeptidomics, metaproteomics and dark proteome
Ontology highlight
ABSTRACT:
INSTRUMENT(S): various instruments
ORGANISM(S): Various Species In Metaproteomics Samples Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
William Noble
PROVIDER: MSV000093980 | MassIVE | Thu Feb 01 23:58:00 GMT 2024
REPOSITORIES: MassIVE
Similar Datasets
Project description:Predicted peptides for the 9-species de novo sequencing benchmark MSV000090982 as described in Yilmaz et al. [Yilmaz2023]. FTP directory contains outputs of 5 de novo peptide sequencing methods on the 9-species benchmark: Casanovo, Casanovo_bm (benchmark), PointNovo, DeepNovo and Novor. [Yilmaz2023] M. Yilmaz*, W. Fondrie*, W. Bittremieux*, R. Nelson, V. Ananth, S. Oh, and W. Noble,"Sequence-to-sequence translation from mass spectra to peptides with a transformer model", bioRxiv, 2023
2024-02-01 | MSV000093979 | MassIVE
Project description:Predicted peptides for the 9-species de novo sequencing benchmark MSV000090982 as described in Yilmaz et al. [Yilmaz2023]. FTP directory contains outputs of 5 de novo peptide sequencing methods on the 9-species benchmark: Casanovo, Casanovo_bm (benchmark), PointNovo, DeepNovo and Novor. Output files for Casanovo contain scan numbers and run names to allow matching to spectra files. [Yilmaz2023] M. Yilmaz*, W. Fondrie*, W. Bittremieux*, R. Nelson, V. Ananth, S. Oh, and W. Noble,"Sequence-to-sequence translation from mass spectra to peptides with a transformer model", bioRxiv, 2023
2024-03-28 | MSV000094434 | MassIVE
Project description:To create a dataset of PSMs that does not exhibit tryptic bias, we selected PSMs with a uniform distribution of amino acids at the C-terminal peptide positions from two datasets: MassIVE-KB [Wang2018] and PROSPECT [Shouman2022]. The MassIVE-KB dataset contains 30 million PSMs and consists entirely of data generated using trypsin; hence, only a small proportion of the MassIVE-KB peptides do not end in K or R, corresponding to those that appear at the C-terminus of the corresponding protein. The PROSPECT dataset is a collection of 61 million PSMs generated from synthetic peptides. To avoid overrepresentation of some peptides in this dataset, we randomly selected at most 100 PSMs per unique peptide, similar to the processing that was done during the creation of the MassIVE-KB dataset. This pre-selection step reduced the size of the PROSPECT dataset to 12.6 million PSMs. Finally, to create a non-enzymatic dataset containing 1 million peptides, we selected 50,000 PSMs for each canonical amino acid. These PSMs were selected at random from MassIVE-KB, then supplemented as necessary from PROSPECT to obtain the desired count (see Yilmaz et al. [Yilmaz2023] Supplementary Table S1). This dataset contained PSMs from 247,859 unique peptides, which were randomly split into training, validation and test sets in the ratio 80/10/10. FTP directory contains the mgf files corresponding to train, validation and test splits.
[Wang2018] M. Wang, J. Wang, J. Carver, B. Pullman, S. Won Cha, N. Bandeira, "Assembling the Community-Scale Discoverable Human Proteome", Cell Systems, Volume 7, Issue 4, 2018.
[Shouman2022] O. Shouman, W. Gabriel, V. Giurcoiu, V. Sternlicht, M. Wilhelm, "PROSPECT: Labeled Tandem Mass Spectrometry Dataset for Machine Learning in Proteomics", NeurIPS Datasets and Benchmarks, 2022
[Yilmaz2023] M. Yilmaz*, W. Fondrie*, W. Bittremieux, R. Nelson, V. Ananth, S. Oh, and W. Noble,"Sequence-to-sequence translation from mass spectra to peptides with a transformer model", bioRxiv, 2023
2024-02-05 | MSV000094014 | MassIVE
Project description:Ocean microbiome dataset published by May et al. [May2016] and the corresponding peptide identifications. The LC-MS/MS spectra are from triplicate acquisitions of peptides, acquisitions 51-53 from the Bering Strait (BSt) and acquisitions 45-47 from the Chukchi Sea (CS). For each sampling location, there are two sets of peptide identifications: one based on a metapeptide database specific to the location and one based on a non-redundant environmental database. Peptide identifications were obtained with Tide search and Percolator as described in Yilmaz et al. [Yilmaz2023].
[May2016] May, D. H. et al. "An Alignment-Free Metapeptide Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing", Journal of Proteome Research, 2016.
[Yilmaz2023] Yilmaz, Melih et al. "Sequence-to-sequence translation from mass spectra to peptides with a transformer model", bioRxiv, 2023.
2024-03-27 | MSV000094415 | MassIVE
Project description:Ocean microbiome dataset published by [May2016] and the corresponding database search results. The LC-MS/MS spectra are from triplicate acquisitions of peptides, acquisitions 51-53 from the Bering Strait (BSt) and acquisitions 45-47 from the Chukchi Sea (CS). For each sampling location, there are two sets of spectrum identifications: one based on a metapeptide database specific to the location (metapeptides_BSt and metapeptides_CS) and one based on a non-redundant environmental database (env_nr). Spectrum identifications were obtained with Tide and Percolator as described in [Yilmaz2023]. Casanovo predictions for this dataset are provided in MSV000093980, alongside Casanovo predictions for other datasets. ________________________________ PUBLICATIONS: [May2016] May, D. H. et al. "An Alignment-Free Metapeptide Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing." Journal of Proteome Research. 2016. [Yilmaz2023] Yilmaz, Melih et al. "Sequence-to-sequence translation from mass spectra to peptides with a transformer model." Nature Communications. 2024. ________________________________ SPECTRUM FILES: The dataset contains the following six spectrum files, three from the Chukchi Sea (2016_Jan_12_QE2_45.mzXML, 2016_Jan_12_QE2_46.mzXML, 2016_Jan_12_QE2_47.mzXML) and three from the Bering Strait (2016_Jan_12_QE3_51.mzXML, 2016_Jan_12_QE3_52.mzXML, 2016_Jan_12_QE3_53.mzXML). ________________________________ FASTA FILES: The dataset containes three protein fasta files: Bering Strait proteins in metapeptides_BSt.fasta, Chukchi Sea proteins in metapeptides_CS.fasta, and the environmental protein database in env_nr.fasta. ________________________________ SEARCH FILES: Associated with each FASTA file is a tide-index log file with names of the form <database>.tide-index.log.txt. The dataset contains Tide output files for 12 searches (six spectrum files, each searched against two databases). For each search, the corresponding tide-search primary output files have names like <sample>.<database>.tide-search.target.txt. There are also corresponding log files and parameter files with names like <sample>.<database>.tide-search.log.txt and <sample>.<database>.tide-search.params.txt. ________________________________ PERCOLATOR FILES: The dataset contains four sets of Percolator output files. The Percolator PSM-level output files are named <location>.<database>.percolator.target.psms.txt, where <location> is "BSt" for Bering Strait and "CS" for Chukchi Sea, and <database> is "metapeptide_BSt", "metapeptide_CS" or "env_nr". The peptide-level output files are <location>.<database>.percolator.target.peptides.txt. The corresponding log files are <location>.<database>.percolator.log.txt. And the lists of peptides accepted at 1% FDR are <location>.<database>.peptides.q01.txt. ________________________________ CASANOVO FILES: Casanovo peptide predictions for this dataset reside in MSV000093980, and they are organized into six mzTab files where each file is named after the corresponding spectrum file. (e.g. 2016_Jan_12_QE2_45.mztab)
2024-05-07 | MSV000094709 | MassIVE
Project description:White grape (Vitis vinifera cv. Furmint) berry samples subjected to natural noble rot were collected in a vineyard in Mád, Hungary (Tokaj wine region). Raw data include grapevine and Botrytis cinerea sequence reads.
2021-11-25 | E-MTAB-11205 | biostudies-arrayexpress
Project description:Noble rot results from atypical infections of ripe grape berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and accumulation of secondary metabolites that enhance wine grape quality. Noble rot-infected berries of Sémillon, a white-skinned variety, were collected over three years from a commercial vineyard at the same time fruit were harvested for botrytized wine production. Transcriptomic and metabolomic data were integrated to identify pathways associated with distinct stages of noble rot. Botrytis induced the expression of known key regulators of pathways in secondary metabolism associated with berry ripening. The activation by Botrytis during noble rot of metabolic pathways associated with berry ripening was further supported by comparisons with transcriptomes of red-skinned varieties at véraison. A prominent and common outcome of noble rot and berry ripening was the enhancement of the phenylpropanoid metabolism. Induced synthesis of stilbenes, flavonoids, and anthocyanins was supported by both transcriptional and metabolite analyses. Enzyme assays and targeted gene expression analyses of samples from the three distinct years confirmed that the activation of central and peripheral phenylpropanoid pathways is a consistent hallmark of noble rot. Finally, we show that the impact of noble rot on grape metabolism is still detectable in botrytized wines. These results demonstrate that despite the late stage of terminal senescence of a plant organ, a biotic stress can cause a major reprogramming of plant metabolism leading, in case of noble rot, to the synthesis of important metabolites for grape berry flavor and aroma.
2015-10-12 | GSE67932 | GEO
Project description:Noble rot results from atypical infections of ripe grape berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and accumulation of secondary metabolites that enhance wine grape quality. Noble rot-infected berries of Sémillon, a white-skinned variety, were collected over three years from a commercial vineyard at the same time fruit were harvested for botrytized wine production. Transcriptomic and metabolomic data were integrated to identify pathways associated with distinct stages of noble rot. Botrytis induced the expression of known key regulators of pathways in secondary metabolism associated with berry ripening. The activation by Botrytis during noble rot of metabolic pathways associated with berry ripening was further supported by comparisons with transcriptomes of red-skinned varieties at véraison. A prominent and common outcome of noble rot and berry ripening was the enhancement of the phenylpropanoid metabolism. Induced synthesis of stilbenes, flavonoids, and anthocyanins was supported by both transcriptional and metabolite analyses. Enzyme assays and targeted gene expression analyses of samples from the three distinct years confirmed that the activation of central and peripheral phenylpropanoid pathways is a consistent hallmark of noble rot. Finally, we show that the impact of noble rot on grape metabolism is still detectable in botrytized wines. These results demonstrate that despite the late stage of terminal senescence of a plant organ, a biotic stress can cause a major reprogramming of plant metabolism leading, in case of noble rot, to the synthesis of important metabolites for grape berry flavor and aroma. The experimental design consists of 4 treatments, berries at 3 distinct stages of noble rot and berries without apparent symptoms of infection. From each treatment a total of 4 biological replicates were sequenced with RNAseq, each replicate corresponded to independent pools of 10-15 berries harvested from adjacent grapevines.
2015-10-12 | E-GEOD-67932 | biostudies-arrayexpress
Project description:Identification of midgut genes with sex-biased transcription and/or splicing under cell-autonomous control of transformer in adult intestinal stem cells Sex differences in physiology are commonly attributed to developmental and/or hormonal factors, but there is increasing realisation that cell-intrinsic mechanisms play important and persistent roles. Here we use the Drosophila melanogaster intestine to investigate the activity and significance of intrinsic sex in an adult somatic organ in vivo. We find that the adult intestinal epithelium is a cellular mosaic of different sex differentiation pathways, and displays extensive sex differences in expression of genes with roles in growth and metabolism. Cell-specific reversals of the sexual identity of adult intestinal stem cells uncover its key roles in controlling organ size, its reproductive plasticity and susceptibility to tumours. Unlike previous examples of sexually dimorphic somatic stem cell activity, the sex differences in intestinal stem cell behaviour arise from intrinsic mechanisms, which control cell cycle duration and involve a new doublesex- and fruitless-independent branch of the sex differentiation pathway downstream of transformer. Together, our findings indicate that the plasticity of an adult somatic organ is reversibly controlled by its intrinsic sexual identity, imparted by a new mechanism that may be active in more tissues than previously recognised. Adult midgut transcriptomes of 15-day-old virgin females were generated by deep sequencing, in triplicate using a Hiseq2000 using paired end 100bp reads. Genotypes were: control, transformer mutant and transformer mutant female in which transformer was re-introduced in adult intestinal stem cells.
2016-02-18 | E-GEOD-74774 | biostudies-arrayexpress