Reanalysis of a proteome-wide level study with MaxLynx
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: 
Sule Yilmaz
LAB HEAD: Juergen Cox
PROVIDER: PXD027188 | Pride | 2022-01-11
REPOSITORIES: Pride
Similar Datasets
Project description:Quantitative proteomics data on Desulfovibrio vulgaris DSM644 grown in lactate-limited chemostats at 3 different rates, exhibiting different magnitudes of S isotope fractionation during dissimilatory sulfate reduction. Protein quantitation by diDO-IPTL peptide isotope labeling (Waldbauer et al. 2017 Anal. Chem.)
2021-07-22 | MSV000087869 | MassIVE
Project description:The field of cross-linking mass spectrometry has matured to a frequently used tool for the investiga-tion of protein structures as well as interactome studies up to a system wide level. The growing com-munity generated a broad spectrum of applications, linker types, acquisition strategies and specialized data analysis tools, which makes it challenging, especially for newcomers, to decide for an appropriate analysis workflow. Therefore, we here present a large and flexible synthetic peptide library as reliable instrument to benchmark cross-linkers with different reactive sites as well as acquisition techniques and data analysis algorithms. Additionally, we provide a tool, IMP-X-FDR, that calculates the real FDR, compares results across search engine platforms and analyses crosslink properties in an auto-mated manner. The library was used with the reagents DSSO, DSBU, CDI, ADH, DHSO and azide-a-DSBSO and data were analysed using the algorithms MeroX, MS Annika, XlinkX, pLink and Max-Lynx. We thereby show that the correct algorithm and search setting choice is highly important to im-prove ID rate and FDR in combination with software and sample-complexity specific score cut-offs. When analysing DSSO data with MS Annika, we reach high identification rates of up to ~70 % of the theoretical maximum (i.e. 700 unique lysine-lysine cross-links) while maintaining a low real FDR of < 3 % at cross-link level and with extraordinary high reproducibility, representatively showing that our test system delivers valuable and statistically solid results.
2022-05-24 | PXD029252 | Pride
Project description:Ex vivo colorectal adenocarcinoma samples were analysed by desorption electrospray ionisation using an Orbitrap mass spectrometer. The samples were analysed in negative mode over the m/z range 600-1000. Some of the samples presented in this dataset were analysed as part of [1]. The study makes available imzML files of profile and centroid mode data, as well as low- and high- resolution optical image files of H&E-stained sections. These files can be found in the zip file named after each tissue section. </p> Ref:</br> [1] Gerbig S, Golf O, Balog J, Denes J, Baranyai Z, Zarand A, Raso E, Timar J, Takats Z. Analysis of colorectal adenocarcinoma tissue by desorption electrospray ionization mass spectrometric imaging. Anal Bioanal Chem. 2012 Jun;403(8):2315-25. doi:10.1007/s00216-012-5841-x. PMID:22447214</br>
2016-04-28 | MTBLS289 | MetaboLights
Project description:LC-MS/MS lipidomics data of Komagataella phaffii recorded on a Q Exactive HF with apex trigger in positive ion mode. Thermo Scientific Accucore C30 column (150 x 2.1 mm, 2.6 um) reverse phase column: A: ACN:H2O 6:4, 10 mM NH4Form, 0.1% FA, B: IPA:ACN 9:1, 10 mM NH4Form, 0.1% FA, 27 min gradient, follows Anal. Chem. 2018, 90 (11), 6494-6501.
2022-07-28 | MSV000090008 | MassIVE
Project description:Anal cancer is a leading neoplasia in people with immune impartments populations, and the lack of an accurate screening test challenges its prevention. Because the bacteria living in the anal epithelium the anal microbiota seems to influence and be influenced by cancer development, specific patterns of anal microbes could help in the diagnosis of precancerous anal lesions. We aimed to discover microbial biomarkers of anal precancer in high-risk populations. We discovered 12 proteins, previously reported to be associated with cancer progression, that were more abundant in the anal bacterial from subjects with precancerous lesions.
2022-12-11 | PXD037268 | Pride
Project description:A comparison of rectal mucosal RNA transcriptome findings between transgender women using feminizing hormone therapy, men who have sex with men engaging in receptive anal intercourse, and males who had never engaged in anal intercourse demonstrates differential gene expression involving pathways critical for mucosal inflammation, suggesting the urgent need for further exploration into the immunologic effects of cross-sex hormone therapy in the rectal mucosa and the potential impact on HIV transmission risk at this site.
2023-03-21 | GSE141785 | GEO
Project description:Chem seq to compare the binding activity of biotynilated drugs.Lurbinectedin and cisplatin comparison
2022-01-29 | GSE190398 | GEO
Project description:Chemerin (CHEM) is a hormone mainly expressed in adipocytes involved in the regulation of energy homeostasis and inflammatory response. CHEM expression has been demonstrated in the structures of the porcine hypothalamic-pituitary-gonadal axis, as well as in the uterus, trophoblasts and conceptuses of pigs. In this study, we performed high-throughput proteomic analyses (Liquid Chromatography with Tandem Mass Spectrometry, LC-MS/MS) to examine the influence of CHEM (400 ng/ml) on differentially regulated proteins (DRPs) in the porcine endometrial tissue explants during implantation (15 to 16 days of gestation). Among all 352 DRPs, 164 were up-regulated and 188 were down-regulated in CHEM-treated group. DRPs were assigned to 47 gene ontology (GO) terms (p-adjusted < 0.05). Validation of four DRPs (IFIT5, TGFβ1, ACO1 and PGRMC1) by Western blot analysis confirmed the veracity and accuracy of LC-MS/MS method used in the present study. We suggest that CHEM, by modulating various protein expressions takes part in the endometrial cell proliferation, migration and invasion at the time of implantation. It also regulates the endometrial immune response, sensitivity to P4 and formation of new blood vessels. Additionally, CHEM appears to be an important factor involved in endothelial cell dysfunction during the pathogenesis of preeclampsia. The identification of a large number of DRPs under the influence of CHEM provides a valuable resource for understanding the molecular mechanisms of this hormone during implantation, which is a prerequisite for better control of pig reproduction.
2022-04-26 | PXD031795 | Pride
Project description:Etiologically linked to HPV infection, malignancies of the anal canal have substantially increased in incidence over the last 20 years. Although most anal squamous cell carcinomas (SCC) respond well to chemoradiotherapy, for undetermined reasons, a subgroup of patients experience a poor outcome. Despite cumulative efforts for discovering independent predictors for overall survival, both nodal status and tumor size are still the only reliable factors predicting patient outcome. In the present study, we correlated both proteomic signatures and clinicopathological features of neoplastic lesions arising from two distinct portions of the anal canal: the lower part (squamous zone) and the more proximal anal transitional zone. Although microdissected cancer cells appeared indistinguishable by morphology (squamous phenotype), unsupervised clustering analysis of the whole proteome significantly highlighted the heterogeneity that exists within anal canal tumors. More importantly, two region-specific subtypes of SCC were revealed. The expression profile (sensitivity/specificity) of several selected biomarkers (keratin filaments) further confirmed the subclassification of anal (pre)cancers based on their cellular origin. Less commonly detected compared to their counterparts located in the squamous mucosa, SCC originating in the transitional zone displayed more frequently a poor or basaloid differentiation and were significantly correlated with reduced disease-free and overall survivals. Taken together, we present for the first time direct evidence that anal canal SCC comprises two distinct entities with different cells of origin, proteomic signatures and survival rates. This study forms the basis for a novel dualistic classification of anal carcinoma with implications for management, outcome expectations and possibly therapeutic approaches.
2016-12-20 | PXD004859 | Pride
Project description:HPV infection results in changes in host gene methylation which, in turn, are thought to contribute to the neoplastic progression of HPV-associated cancers. The objective of this study was to identify joint and disease-specific genome-wide methylation changes in anal and cervical cancer as well as changes in high-grade pre-neoplastic lesions. Formalin-fixed paraffin-embedded (FFPE) anal tissues (n=143; 99% HPV+) and fresh frozen cervical tissues (n=28; 100% HPV+) underwent microdissection, DNA extraction, HPV genotyping, bisulfite modification, DNA restoration (FFPE) and analysis by the Illumina HumanMethylation450 Array.
2021-11-29 | GSE186835 | GEO