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ProteomicsAssessing protein sequence database suitability using de novo sequencing
The analysis of samples from unsequenced and/or understudied species as well as samples where the proteome is derived from multiple organisms poses two key questions. The first is whether the proteomic data obtained from an unusual sample type even contains peptide tandem mass spectra. The second ...
ORGANISM(S): glacier metagenome Hydrolagus colliei Diaphorina citri (Asian citrus psyllid) Homo sapiens (Human) marine metagenome Ursus deningeri Caenorhabditis elegans Leucoraja erinacea 
2019-11-20 | PXD015083 | Pride
Fasta Proteomics Metaproteomics 
ProteomicsThe molecular basis of integrated stress response silencing
Chronic stress response activation impairs cell survival and causes devastating degenerative di-seases. To counteract this, cells deploy dedicated silencing factors, such as the E3 ligase SIFI that terminates the mitochondrial stress response. How a single enzyme can sense stress across cellular sca...
ORGANISM(S): Homo sapiens (Human) 
2025-04-16 | PXD055759 | Pride
Sifi Xl-ms Mass spectrometry Ubiquitin E3 ligase Bs3 
ProteomicsComprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries
Raw DDA and DIA data to support Searle et al. 2018. Comprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries. bioRxiv doi:10.1101/277822
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2018-08-08 | MSV000082805 | MassIVE
ProteomicsHighly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment
Targeted mass spectrometry methods produce high quality quantitative data in terms of limits of detection and dynamic range, at the cost of a substantial compromise in throughput compared to methods such as data independent and data de-pendent acquisition. The logistical and experimental issues inhe...
ORGANISM(S): Homo Sapiens 
2021-01-24 | PXD018675 | panorama
ProteomicsMag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome
Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent ~1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a “liquid biopsy,” wh...
ORGANISM(S): Homo Sapiens 
PXD042947 | panorama
MetabolomicsFecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial

Fecal microbiota transplantation (FMT) represents a potential strategy to overcome resistance to immune checkpoint inhibitors in patients with refractory melanoma; however, the role of FMT in first-line treatment settings has not been evaluated. We conducted a multicenter phase I trial combining ...

2025-02-27 | MTBLS711 | MetaboLights
UnknownA Framework for Quality Control in Quantitative Proteomics.
Not available
S-EPMC11973981 | biostudies-literature
UnknownA framework for quality control in quantitative proteomics.
Not available
S-EPMC11030400 | biostudies-literature
ProteomicsImproved analysis of crosslinking mass spectrometry data with Kojak 2.0, advanced by integration into the Trans-Proteomic Pipeline
Fragmentation ion spectral analysis of chemically crosslinked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which...
ORGANISM(S): Bos taurus (Bovine) Saccharomyces cerevisiae (Baker's yeast) 
2023-01-18 | PXD037492 | Pride
Kojak Crosslinking mass spectrometry Proteomics Software tools Protein interaction Peptideprophet Xl-ms Trans-proteomic pipeline Computational proteomics Iprophet 
ProteomicsMultiplexed, scheduled high resolution sMRM-HR acquisition on full scan MS/MS instruments
Advances in software and high resolution, high mass accuracy mass spectrometers have expanded their functionality beyond traditional data dependent acquisition (DDA) methods. Using a single platform, an orthogonal quadrupole time-of flight (QqTOF) mass spectrometer, the TripleTOF 5600, we have inve...
ORGANISM(S): Bos Taurus (ncbitaxon:9913) Escherichia Coli (ncbitaxon:562) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2015-03-10 | MSV000079077 | MassIVE
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