ProCon — PROteomics CONversion tool

Mayer, Gerhard; Stephan, Christian; Meyer, Helmut E.; Köhl, Michael; Marcus, Katrin; Eisenacher, Martin

doi:10.1016/j.jprot.2015.06.015

Cited by 12 publications

(9 citation statements)

References 57 publications

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“…ProCon—PROteomics CONversion tool (ver. 0.9.641) was used for the necessary conversion of Proteome Discoverer result files into the mzIdentML standard format ( 26 ).…”

Section: Methodsmentioning

confidence: 99%

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression

et al. 2017

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Interferons (IFNs) are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction). In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive analysis revealed important insights into the human IFN-regulated proteome and its dynamics of protein induction and repression. Interestingly, the new class of IFN-repressed genes comprises known host factors for highly relevant pathogens such as HIV, dengue virus, and hepatitis C virus.

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“…ProCon—PROteomics CONversion tool (ver. 0.9.641) was used for the necessary conversion of Proteome Discoverer result files into the mzIdentML standard format ( 26 ).…”

Section: Methodsmentioning

confidence: 99%

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression

et al. 2017

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“…Conversion of msf files (result files of Proteome Discoverer) into the mzIdentML standard format was conducted using ProCon -PROteomics CONversion tool (ver. 0.9.641) (16). /dox ϩ ) exosomes were analyzed as biological replicates to increase the reliability and achieve adequate predictive power for global label-free quantitative proteomics profiling.…”

Section: Methodsmentioning

confidence: 99%

Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line

Jia

Chen

Megger

et al. 2017

Molecular & Cellular Proteomics

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Hepatitis B virus (HBV) infection is a major health problem worldwide. Recent evidence suggests that some viruses can manipulate the infection process by packing specific viral and cellular components into exosomes, small nanometer-sized (30-150 nm) vesicles secreted from various cells. However, the impact of HBV replication on the content of exosomes produced by hepatocytes has not been fully delineated. In this work, an HBV-inducible cell line HepAD38 was used to directly compare changes in the protein content of exosomes secreted from HepAD38 cells with or without HBV replication. Exosomes were isolated from supernantants of HepAD38 cells cultured with or without doxycycline (dox) and their purity was confirmed by transmission electron microscopy (TEM) and Western immunoblotting assays. Ion-intensity based label-free LC-MS/MS quantitation technologies were applied to analyze protein content of exosomes from HBV replicating cells [referred as HepAD38 (dox)-exo] and from HBV nonreplicating cells [referred as HepAD38 (dox)-exo]. A total of 1412 exosomal protein groups were identified, among which the abundance of 35 proteins was significantly changed following HBV replication. Strikingly, 5 subunit proteins from the 26S proteasome complex, including PSMC1, PSMC2, PSMD1, PSMD7 and PSMD14 were consistently enhanced in HepAD38 (dox)-exo. Bioinformatic analysis of differential exosomal proteins confirmed the significant enrichment of components involved in the proteasomal catabolic process. Proteasome activity assays further suggested that HepAD38 (dox)-exo had enhanced proteolytic activity compared with HepAD38 (dox)-exo. Furthermore, human peripheral monocytes incubated with HepAD38 (dox)-exo induced a significantly lower level of IL-6 secretion compared with IL-6 levels from HepAD38 (dox)-exo. Irreversible inhibition of proteasomal activity within exosomes restored higher production of IL-6 by monocytes, suggesting that transmission of proteasome subunit proteins by HepAD38 (dox)-exo might modulate the production of pro-inflammatory molecules in the recipient monocytes. These results revealed the composition and potential function of exosomes produced during HBV replication, thus providing a new perspective on the role of exosomes in HBV-host interaction.

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“…The .msf files obtained in Proteome Discoverer were converted into the mzIdentML standard format using ProCon PROteomics Conversion tool version 0.9.718. 43…”

Section: Protein Identification and Quantificationmentioning

confidence: 99%

Integrated Fourier Transform Infrared Imaging and Proteomics for Identification of a Candidate Histochemical Biomarker in Bladder Cancer

Witzke

Großerueschkamp

Jütte

et al. 2019

The American Journal of Pathology

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Histopathological differentiation between severe urocystitis with reactive urothelial atypia and carcinoma in situ (CIS) can be difficult, particularly after a treatment that deliberately induces an inflammatory reaction, such as intravesical instillation of Bacillus Calmette-Guèrin. However, precise grading in bladder cancer is critical for therapeutic decision making and thus requires reliable immunohistochemical biomarkers. Herein, an exemplary potential biomarker in bladder cancer was identified by the novel approach of Fourier transform infrared imaging for label-free tissue annotation of tissue thin sections. Identified regions of interest are collected by laser microdissection to provide homogeneous samples for liquid chromatographyetandem mass spectrometryebased proteomic analysis. This approach afforded label-free spatial classification with a high accuracy and without interobserver variability, along with the molecular resolution of the proteomic analysis. Cystitis and invasive highgrade urothelial carcinoma samples were analyzed. Three candidate biomarkers were identified and verified by immunohistochemistry in a small cohort, including low-grade urothelial carcinoma samples. The best-performing candidate AHNAK2 was further evaluated in a much larger independent verification cohort that also included CIS samples. Reactive urothelial atypia and CIS were distinguishable on the basis of the expression of this newly identified and verified immunohistochemical biomarker, with a sensitivity of 97% and a specificity of 69%. AHNAK2 can differentiate between reactive urothelial atypia in the setting of an acute or chronic cystitis and nonmuscle invasive-type CIS. (Am J Pathol 2019, 189: 619e631; https://doi.org/10. 1016/j.ajpath.2018.11.018) Bladder cancer is the second most common urogenital malignancy, with approximately 430,000 new cases diagnosed worldwide in 2012. 1,2 Approximately 70% to 75% of patients are newly diagnosed with nonmuscle invasive, mostly low-grade bladder cancer, whereas 25% to 30% of de novo diagnoses are high-grade bladder cancer at the stage of infiltration of the muscularis, with metastases observed in 10% of cases. 3e5 A significant percentage (50% to 70%) of patients diagnosed with nonmuscle invasive cancer will have multiple recurrences, and 10% to 15% will even progress to invasion. 3,6,7 A special case of bladder cancer is carcinoma in situ (CIS), which is a flat, noninvasive tumor with a rate of progression to an invasive state of approximately 54%. 8

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ProCon — PROteomics CONversion tool

Cited by 12 publications

References 57 publications

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression

Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line

Integrated Fourier Transform Infrared Imaging and Proteomics for Identification of a Candidate Histochemical Biomarker in Bladder Cancer

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