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ProteomicsMetaproteomic analysis using the Galaxy framework
Metaproteomics characterizes proteins expressed by microorganism communities (microbiome) present in environmental samples or a host organism (e.g. human), revealing insights into the molecular functions conferred by these communities. Compared to conventional proteomics, metaproteomics presents un...
ORGANISM(S): Homo sapiens (Human) 
2015-07-02 | PXD001655 | Pride
Metaproteomics   workflows. 
ProteomicsHuman oral cancer brush biopsy iTRAQ
iTRAQ-based comparison of proteins derived from oral cells collected by brush biopsy. Protein abundance levels compared between oral pre-malignant cells, oral cancer cells and healthy normal cells, all collected from human patients. Two separate iTRAQ labeled biological replicate analyses were con...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-07-22 | MSV000079994 | MassIVE
ProteomicsQuantitative proteogenomic characterization of inflamed murine colon tissue using an integrated discovery, verification, and validation proteogenomic workflow
Rag2-/-Il10-/- mice were subjected to infection by Helicobacter hepaticus and allowed to develop long-term infections. Proximal colon tissue was then harvested from the mice for analysis. RNA was isolated from the samples and submitted for transcriptomic analysis; this data was then used to create a...
ORGANISM(S): Mus musculus (Mouse) 
2022-05-19 | PXD028407 | Pride
Mouse Tmt Prm Proximal colon Orbitrap Dda 
ProteomicsData for manuscript, “An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples”
Clinical BALF samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease. However, MS based proteomic analysis of BALF is impeded by the dynamic range of protein abundance, and potential for interfering contaminants. We have developed a workflow...
ORGANISM(S): Homo sapiens (Human) 
2023-04-05 | PXD038522 | Pride
Bronchoalveolar lavage fluid  balf  quantitative proteomics  mass spectrometry  sample preparation  lung disease 
ProteomicsData-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome
Metaproteomics used bottom-up mass spectrometry to detect and quantify the proteins present in microbiome samples. Historically, the methodology of choice in these analyses has been Data-Dependent Acquisition mass spectrometry (DDA-MS). In this manuscript we see sought to evaluate the reproducibilit...
ORGANISM(S): Enterobacteria phage ES18 Thermus thermophilus Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) Bacteria Stenotrophomonas maltophilia Nitrosospira multiformis Anthracocystis tumefaciens Alteromonas macleodii Archaea Salmonella phage P22 Paracoccus denitrificans Pseudomonas denitrificans (nom. rej.) unclassified Bacillus subtilis group Roseobacter Cupriavidus metallidurans Chlamydomonas reinhardtii Nitrososphaera viennensis Enterobacteria phage f2 Nitrosomonas ureae Escherichia phage M13 Chromobacterium violaceum unclassified Pseudomonas fluorescens group Escherichia coli Pseudomonas cf. pseudoalcaligenes Rhizobium leguminosarum Desulfovibrio vulgaris str. Hildenborough Staphylococcus aureus Paraburkholderia xenovorans 
2024-12-19 | PXD054415 | Pride
Data independent acquisition Microbiome Metaproteomics 
ProteomicsMethod to identify novel proteoform peptides from salivary supernatant.
We describe the use Galaxy framework to facilitate complete proteogenomic analysis for a representative salivary dataset. We demonstrate how Galaxy’s many features make it a unique and ideal solution for proteogenomic analysis. We highlight Galaxy’s flexibility by creating a modular workflow incor...
ORGANISM(S): Homo sapiens (Human) 
2015-01-05 | PXD000991 | Pride
Proteoforms Proteogenomics Saliva 
ProteomicsMetaproteomic analysis of nasopharyngeal swab samples to identify microbial peptides and potential co-infection status in COVID-19 patients
Respiratory infections disrupt the microbiota in the upper respiratory tract (URT), putting patients at a risk for subsequent infections. During the pandemic, cases of COVID-19 were aggravated by secondary infections because of impaired immunity and medical interventions, which was clearly evident i...
ORGANISM(S): Homo Sapiens 
2025-11-01 | PXD039598 | panorama
ProteomicsCritical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows
Metaproteomics, the study of the collective proteome within a microbial ecosystem, has substantially grown over the past few years. This growth comes from the increased awareness that it can powerfully supplement metagenomics and metatranscriptomics analyses. Although metaproteomics is more challeng...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) 
2022-06-08 | MSV000089620 | MassIVE
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