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Metaproteomes of cyanobacterial consortium collected from photobioreactors enriched from soda lake microbial mats in BC, Canada

ABSTRACT: In this work we used metaproteomics to study the effect of pH and nitrogen source on cyanobacterial growth of the laboratory cultures. The database for protein identification was obtained from assembled metagenomes.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Oscillatoriaceae Cyanobacterium

SUBMITTER: Maryam Ataeian

LAB HEAD: Marc Strous

PROVIDER: PXD024393 | Pride | 2021-11-02

REPOSITORIES: Pride

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Proteomes of twenty bacterial, archaeal and eukaryotic species for bench marking of Direct Protein-SIF (stable carbon isotope fingerprinting proteomics)

Project description:We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. To benchmark this method, we measured twenty pure culture species using the Direct Protein-SIF method as well as Isotope Ratio Mass Spectrometry. Some of the pure cultures were measured in technical replicates to see how consistent Protein-SIF measurements are between mass spec runs. This submission thus contains 29 raw files for the pure cultures. See table in the submission for details of which species was measured for which .raw file. We also included the Direct Protein-SIF specific isotope pattern files as well as the .mzML files and PSM files required as input for the Direct Protein-SIF software. In addition to the pure culture a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are also included in this submission (see publication for details on how the reference material is used to calibrate the method).

2018-05-21 | PXD006762 | Pride

Metaproteomics of the marine gutless oligochaete Olavius algarvensis and its symbionts to determine stable isotope fingerprints using Direct Protein-SIF

Project description:We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. We validated and tested the method extensively using pure cultures (PXD006762) and mock communities (PXD006118, https://www.ebi.ac.uk/pride/archive/projects/PXD006118). As a case study we applied Direct Protein-SIF to the Olavius algarvensis symbiosis. Olavius algarvensis is a marine worm that lives in shallow-water sediments off the coast of Elba, Italy. The worm has no digestive and excretory system, instead it harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (http://www.pnas.org/content/109/19/E1173.short). For this project we generated metaproteomes of 14 O. algarvensis individuals. A total of 18 LC-MS/MS runs were generated. For Direct Protein-SIF the data from all runs was combined. In this submission we are including the Direct Protein-SIF specific isotope pattern file as well as the .mzML files and PSM file required as input for the Direct Protein-SIF software (Calis-p). In addition to the Olavius algarvensis samples a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are available through project PXD006762 (see publication for details on how the reference material is used to calibrate the method).

2018-05-21 | PXD007510 | Pride

Proteomics of Ca. Riegeria standrea – the chemosynthetic symbionts of the marine flatworm Paracatenula from the Bay of Sant´Andrea (Elba, Italy)

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Stable isotope probing with 13C-labeled bicarbonate/proteomics of cyanobacterial consortium collected from photobioreactors enriched from soda lake microbial mats in BC, Canada

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Metaproteomes of phototrophic mats from four soda lakes found in the Cariboo Plateau region of British Columbia, Canada

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2019-07-29 | PXD011230 | Pride

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2017-05-12 | PXD006343 | Pride

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2022-02-16 | PXD024288 | Pride

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2017-05-12 | PXD006118 | Pride

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2018-05-17 | PXD007623 | Pride

Labeling of Bacillus subtilis and Escherichia coli to saturation with different percentages of 13C2 labeled glucose for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli and Bacillus subtilis cultures were labeled with different percentages of single-carbon 13C glucose (13C2). Cultures of B. subtilis and E. coli were grown in Bacillus minimal medium or M9 minimal medium (E. coli) in which a percentage of the glucose was replaced with 13C2 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C2 glucose were added 0, 0.01, 0.025, 0.1, 0.25, 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

2022-12-30 | PXD024285 | Pride

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