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MTB_starved_cultureFiltrateSamples

ABSTRACT: Triplicate culture filtrate samples of normal (log phase) and PBS cultured (starvation) M. tuberculosis were separated by SDS-PAGE, and 10 bands were excised from each lane after staining with Coomassie R-250. In-gel trypsin digestion was performed on gel bands followed by nanoLC. Eluting peptides were then analyzed on an LTQ FT instrument.

REANALYSIS of: PXD000111

INSTRUMENT(S): LTQ FT

ORGANISM(S): Mycobacterium Tuberculosis

SUBMITTER: Ida Rosenkrands

PROVIDER: PAe003970 | PeptideAtlas | 2013-12-31

REPOSITORIES: PeptideAtlas

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			Action	DRS
	PAe003970_7857_tandem.params	Other
	PAe003970_RAW_201302121046.tar.gz	Other
	PAe003970_README	Other
	PAe003970_Search_Results_7857_201302121050.properties	Other
	PAe003970_Search_Results_7857_201302121050.tar.gz	Other

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Publications

Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems.

Albrethsen Jakob J Agner Jeppe J Piersma Sander R SR Højrup Peter P Pham Thang V TV Weldingh Karin K Jimenez Connie R CR Andersen Peter P Rosenkrands Ida I

Molecular & cellular proteomics : MCP 20130123 5

In order to successfully enter the latent stage, Mycobacterium tuberculosis must adapt to conditions such as nutrient limitation and hypoxia. In vitro models that mimic latent infection are valuable tools for describing the changes in metabolism that occur when the bacterium exists in a non-growing form. We used two complementary proteomic approaches, label-free LC-MS/MS analysis and two-dimensional difference gel electrophoresis, to determine the proteome profile of extracellular proteins from ...[more]

PMID: 23345537

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Mycobacterium tuberculosis culture filtrate LC-MS/MS

Project description:Triplicate culture filtrate samples of normal (log phase) and PBS cultured (starvation) M. tuberculosis were separated by SDS-PAGE, and 10 bands were excised from each lane after staining with Coomassie R-250. In-gel trypsin digestion was performed on gel bands followed by nanoLC. Eluting peptides were then analyzed on an LTQ FT instrument, and the resulting raw files were searched with Sequest (part of Proteome Discoverer) against an M. tuberculosis H37Rv database (downloaded from the Sanger Centre). The final combined dataset comprised 12,399 unique peptides derived from 1,362 proteins, each identified by a minimum of two distinct peptides.

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Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae

Project description:Proteomics is a high-throughput technology which has been developed with the aim of investigating the maximum number of proteins in cells in a given experiment. However, protein discovery and data generation vary in depth and coverage when different technical strategies are selected. In this study, three different sample preparation approaches, and peptide or protein fractionation methods, were applied to identify and quantify proteins from log-phase yeast lysate: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), filter-aided sample preparation coupled with gas phase fractionation (FASP-GPF), and FASP - high pH reversed phase fractionation (HpH). Fractions were initially analyzed and compared using nanoflow liquid chromatography – tandem mass spectrometry (nanoLC-MS/MS) employing data dependent acquisition on a linear ion trap instrument. The number of fractions and analytical replicates was adjusted so that each experiment used a similar amount of mass spectrometric instrument time. A second set of experiments was performed using a Q Exactive Orbitrap instrument, comparing FASP-GPF, SDS-PAGE and FASP-HpH. Compared with results from the linear ion trap mass spectrometer, the use of a Q Exactive Orbitrap mass spectrometer enabled a small increase in protein identifications, and a very large increase in peptide identifications. This shows that the main advantage of using the higher resolution instrument is in increased proteome coverage. A total of 1035, 1357 and 2134 proteins were separately identified by FASP-GPF, SDS-PAGE, and FASP-HpH. Combining results from the Orbitrap experiments, there were a total of 2269 proteins found, with 94% of them identified using the FASP-HpH method. Therefore, the FASP-HpH method is the optimal choice among these approaches, when applied to this type of sample.

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MS analysis of BCG and recombinant BCG "70C-RBD"

Project description:BCG and recombinant BCG "70C-RBD" were cultured in Sauton media. Culture filtrate and cells lysate were separated by SDS-PAGE. The bands at 40kDa and 60kDa were excised and proteins were reduced and alkylated. In-gel digestion (Trypsin) was performed. The samples were analyzed by TripleTOF5600+ conjugating with nanoLC column in data-dependent mode.

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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data

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Membrane Fraction Complexome of Nitrososphaera viennensis with BN-PAGE and Examination of the Archaeal Ammonia Monooxygenase Complex via SDS-Tricine-PAGE

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