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Post-doctoral position

"Application of DeepProt open mass search algorithms to bottom-up proteomics data"

Location: Plateforme d’Analyse Protéomique de Paris Sud-Ouest (PAPPSO), Gif-sur-Yvette (France)

Date: from automun 2019 to spring 2021 (18 months)

Salary: 27-30 K€ (gross salary)

Key words: proteomics, LC-MS/MS, mass spectra interpretation, open mass search, protein identification, protein modifications

Context:

Bottom-up proteomics generates tens of thousands of experimental spectra in a single LC-MS/MS injection. Software is essential to get information from so huge raw data, but at the moment on average 50 to 75% of the spectra remain uninterpreted after analysis. Modifications displayed by proteins are the most widespread hypothesis to explain this low rate. The ANR project DeepProt aims at developing new open mass search algorithms to more exhaustively interpret the set of experimental spectra generated by proteomics experiments - even those from complex metaproteomics studies - and next to deduce the list of proteins present in the analyzed mixture with detailed information about their post-translational modifications (PTM).

Objective:

The objective of this post-doctoral position is to define the fields of application in which the algorithms developed in the context of the DeepProt project are the most effective and to bring the proof of concept that these algorithms are highly effective to interpret protein mass modifications. To this end, several datasets are available at PAPPSO, including a metaproteomic dataset and datasets containing proteins with known modifications (either PTMs or amino-acid changes resulting from allelic modifications in the sequences of the encoding gene).

Environment:

PAPPSO (www.pappso.inra.fr) is a proteomic facility that aim to provide research teams with high skills and new-advanced equipments in the field of proteomics. It is more particularly specialized in high throughput proteomics (quantitative analysis of large cohorts of samples) and in the analysis of highly complex samples (metaproteomics). PAPPSO also develops bioinformatics tools that allow the processing of these experiments and provides assistance to users for data interpretation. PAPPSO gathers two sites distant from 8 kms: one located at the Moulon (Gif-sur-Yvette) in the Quantitative Genetics and Evolution laboratory (GQE-Le Moulon, 98 people) and the other one in Jouy-en-Josas in the MICALIS Institute (Food and Gut Microbiology for Human Health, 350 people). Each site has developed specificities related with its home laboratory. The Moulon site, where the successful applicant will be based, has been specialized in plant proteomics for a long time.

Candidates:

Applicants should hold a PhD or a doctoral degree and show a sound expertise in comprehensive analysis of proteomics data and/or in bioinformatics and bioanalysis. Statistical skill would be much appreciated.

Interested candidates are encouraged to submit a cover letter, a CV with a list of publications and contact details of 2-3 referees by email to michel.zivy@inra.fr and melisande.blein-nicolas@inra.fr. 

Position title: Post-doctoral fellowship in proteomics of Retinal Pigment Epithelium

Company: National Eye Institute, National Institutes of Health

Location: Bethesda, Maryland, USA

Summary of position: The Redmond lab (Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, NIH) is seeking to recruit an outstanding post-doctoral fellow to study proteomics of the retinal pigment epithelium (RPE) of the outer retina. We investigate the biochemistry and molecular biology of the retina and retinal pigment epithelium (RPE), including RPE65 and visual cycle retinoid metabolism in the RPE, and other characteristic processes of the RPE essential to vision. The RPE is a highly metabolically and physiologically specialized tissue with metabolic processes important to continuing vision, not found in other tissues, even elsewhere in the eye. Many blinding diseases (inherited and age-related) involve derangement of these key RPE processes. As much of the basic fundamentals remains unknown, we are investigating in depth the sub-proteomes of the RPE to better understand their role in health and blinding disease.

Qualifications: Candidates must hold a PhD or MD/PhD in a cognate field, within three years of degree being awarded; must have first authorship on at least one peer-reviewed publication; have strong training in biochemistry/proteomics/structural biology with experience in protein/cellular fractionation/purification, proteomics and mass spectrometry; have excellent writing and communications skills; and must be highly motivated to develop technical expertise and career-enhancing skills. The ability to work independently as well as part of a team is important as we are a highly collaborative lab.

Links, etc: https://irp.nih.gov/pi/t-michael-redmond; https://www.researchgate.net/profile/Thomas_Redmond

Link to full description: https://www.training.nih.gov/postdoc_jobs_nih/view/_31/6728/Proteomics_of_Retinal_Pigment_Epithelium

Contact information: Interested candidates can send an email of interest to redmondd@nei.nih.gov with a CV, names and contact info for 3 references, a one-page statement of interest, and a summary of previous research experience and future career interests.

Area: Protease biology and proteomics.
Duration: 1 year; based on performance can be extended for up to 3 years
Start date: Application review will begin immediately and will continue until the position is filled.
Stipend: $45,000 Canadian per year plus benefits.

Position Description:
The Brömme Lab at the University of British Columbia is seeking a highly motivated, enthusiastic, and independent-thinking postdoctoral candidate studying the cellular ligase activities of protease. The candidate will work under the direct supervision of Dr. Dieter Brömme and will use cellular, biochemical, protein chemistry, and mass-spectrometry-based proteomics approaches. The candidate will be part of a collaborative team. The minimum academic requirement is a PhD in a life science subject received not more than 2 years ago.

Click here for qualification and submission details...