Proteomic responses to a methyl viologen-induced oxidative stress in the wild type and FerB mutant strains of Paracoccus denitrificans

Pernikářová, Vendula; Sedláček, Vojtěch; Potěšil, David; Procházková, Iva; Zdráhal, Zbyněk; Bouchal, Pavel; Kučera, Igor

doi:10.1016/j.jprot.2015.05.002

Cited by 12 publications

(21 citation statements)

References 48 publications

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“…The samples were then mixed, dried in a centrifugal vacuum concentrator, and fractionated using hydrophilic chromatography (HILIC) as previously described. [ 23 ] Fourteen fractions were collected in a peak‐dependent manner.…”

Section: Methodsmentioning

confidence: 99%

Transgelin Silencing Induces Different Processes in Different Breast Cancer Cell Lines

et al. 2020

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Transgelin is a protein reported to be a marker of several cancers. However, previous studies have shown both up‐ and down‐regulation of transgelin in tumors when compared with non‐tumor tissues and the mechanisms whereby transgelin may affect the development of cancer remain largely unknown. Transgelin is especially abundant in smooth muscle cells and is associated with actin stress fibers. These contractile structures participate in cell motility, adhesion, and the maintenance of cell morphology. Here, the role of transgelin in breast cancer is focused on. Initially, the effects of transgelin on cell migration of the breast cancer cell lines, BT 549 and PMC 42, is studied. Interestingly, transgelin silencing increased the migration of PMC 42 cells, but decreased the migration of BT 549 cells. To clarify these contradictory results, the changes in protein abundances after transgelin silencing in these two cell lines are analyzed using quantitative proteomics. The results confirmed the role of transgelin in the migration of BT 549 cells and suggest the involvement of transgelin in apoptosis and small molecule biochemistry in PMC 42 cells. The context‐dependent function of transgelin reflects the different molecular backgrounds of these cell lines, which differ in karyotypes, mutation statuses, and proteome profiles.

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Section: Methodsmentioning

confidence: 99%

Transgelin Silencing Induces Different Processes in Different Breast Cancer Cell Lines

et al. 2020

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“…A similar setup was used for proteomic analysis of Paracoccus denitrificans. With iTRAQ labeling, the total number of fractions was 32, and the number of protein identification was 2627, covering 52.3% of the putative proteome of the bacteria [68]. Setups and performance of some outstanding 3D-LC systems are summarized in Table 1.…”

Section: Offline 3d-lc Systemsmentioning

confidence: 99%

“…As a result, 3D-LC methods often require a large amount of sample. It is particularly prominent in offline systems with the use of several hundred micrograms [61] to microgram [68] of peptide sample. However, the development of integrated devices has intensely reduced the sample amount.…”

Section: Author's Outlook and Concluding Remarksmentioning

confidence: 99%

Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics

Duong

Park

Lee

2020

IJMS

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Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.

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“…Metódou RC-DC (Bio-Rad, USA) bola zmeraná koncentrácia proteínu v supernatante a 100 µg proteínového lyzátu bolo odobraných na proteolytické štiepenie. Proteolytické štiepenie a purifikácia peptidov z MCF-7 boli prevedené podľa Pernikářová et al [7].…”

Section: Materiál a Metódyunclassified

Building Mass Spectrometry Spectral Libraries of Human Cancer Cell Lines

Faktor¹,

Bouchal²

2016

Klin Onkol

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Regionální centrum aplikované molekulární onkologie, Masarykův onkologický ústav, Brno Súhrn Východiská: Kvantifikácia proteínov v modelových nádorových bunečných líniách a v nádorových tkanivách je často predmetom onkologického výskumu. Metóda SWATH (sequential windowed acquisition of all theoretical fragment ion spectra), novinka v kvantitatívnej onkoproteomike, získava čoraz väčšiu popularitu, pretože umožňuje kvantifikáciu všetkých proteínov zaznamenaných v spektrálnej knižnici. Spektrálna knižnica obsahuje fragmentačné informácie o každom detekovateľnom proteíne vo vzorke. Dôkladná príprava spektrálnej knižnice výrazne vylepší kvantifikáciu obzvlášť nízkoabundantných proteínov, ktoré často zohrávajú výnamnú úlohu v nádorových ochoreniach. Cieľ: V tomto článku sa venujeme optimalizácii prípravy spektrálnej knižnice s cieľom maximalizovať počet kvantifikovateľných proteínov v modelovej bunečnej línii MCF-7 odvodenej od karcinómu prsníka. Experiment je zameraný na optimalizáciu postupu prípravy vzorky pred vstupom do hmotnostného spektrometru, kde bol skúmaný vplyv zloženia lyzačného pufru, vplyv postupu rozpúšťania peptidov a vplyv materiálu mikroskúmaviek na počet proteínov v spektrálnej knižnici. V neposlednom rade boli optimalizované aj parametre merania na hmotnostnom spektrometri pre získavanie dát do spektrálnej knižnice. Záver: Dôslednou optimalizáciou postupu sa podarilo pripraviť spektrálnu knižnicu obsahujúcu fragmentačné informácie o 1 653 proteínoch (FDR < 1%) z 1 µg lyzátu MCF-7. Hlavným prínosom optimalizácie postupu prípravy spektrálnej knižnice je rozšírenie pokrytia proteómu vo SWATH digitálnych bio bankách umožňujúcich kvantifikáciu ľubovoľného proteínu vo fyzicky už nedostupných vzorkách. Kvalitné spektrálne knižnice by mohli v budúcnosti zohrávať kľúčovú úlohu pri tvorbe digitálnych fingerprintov proteómu pa cientov. Kľúčové slová nádorové biomarkery-hmotnostná spektrometria-proteomika-digitálna bio banka-SWATH-kvantifikácia proteínov Summary Background: Cancer research often focuses on protein quantification in model cancer cell lines and cancer tissues. SWATH (sequential windowed acquisition of all theoretical fragment ion spectra), the state of the art method, enables the quantification of all proteins included in spectral library. Spectral library contains fragmentation patterns of each detectable protein in a sample. Thorough spectral library preparation will improve quantitation of low abundant proteins which usually play an important role in cancer. Aim: Our research is focused on the optimization of spectral library preparation aimed at maximizing the number of identified proteins in MCF-7 breast cancer cell line. First, we optimized the sample preparation prior entering the mass spectrometer. We examined the effects of lysis buffer composition, peptide dissolution protocol and the material of sample vial on the number of proteins identified in spectral library. Next, we optimized mass spectrometry (MS) method for spectral library data acquisition. Conclusion: Our thorough optimized...

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Proteomic responses to a methyl viologen-induced oxidative stress in the wild type and FerB mutant strains of Paracoccus denitrificans

Cited by 12 publications

References 48 publications

Transgelin Silencing Induces Different Processes in Different Breast Cancer Cell Lines

Transgelin Silencing Induces Different Processes in Different Breast Cancer Cell Lines

Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics

Building Mass Spectrometry Spectral Libraries of Human Cancer Cell Lines

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