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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...

Proteomics Core Specialists Position
Institute of Plan and Microbial Biology, Academia Sinica, Taiwan

The Institute of Plant and Microbial Biology (IPMB), Academia Sinica, Taipei, Taiwan (http://ipmb.sinica.edu.tw/), is inviting applications for the position of a certified staff to manage the proteomics core laboratory, with the title of Assistant, Associate, or Full Research Specialist.

Interested candidates should hold a Ph.D. degree or an equivalency diploma, with in‐depth experience and broad knowledge in protein-related research such as proteomics, protein chemistry/structure, and mass spectrometry. Excellent analytical skills and communication capacities in both Chinese and English are required. The successful candidate is expected to manage and lead at least one supporting staff in providing proteomics and protein analysis service and carrying out research together with scientists at IPMB.

Academia Sinica, the foremost academic institution in Taiwan, comprises 31 research institutes/centers and provides an active research environment. IPMB, consisting of 27 Principal Investigators, is a research institute focusing on studies of functions of plants and plant-related microbes. IPMB also maintains well-equipped core facilities managed by Research Specialists/Assistants including Proteomics, Genomics, Metabolomics, Bioinformatics, Cell Biology and Imaging Facilities.

The application folder should include 1) a cover letter, 2) a curriculum vitae, 3) a statement of research accomplishments, 4) a future R&D and management plan, and 5) reprints of up to five representative publications. The application folder (in PDF format) and, separately, three letters of recommendation should be sent via email to:

Dr. Erh-Min Lai, Chair of Recruitment Committee|
c/o Ms. Hsiao-Yun Wang (email: ipmbsearch@gate.sinica.edu.tw)
Institute of Plant and Microbial Biology, Academia Sinica
128, Sec 2, Academia Rd, Nankang, Taipei, Taiwan 11529

To ensure full review, applications should be received before August 31, 2019.

Position title: Postdoc in Advanced Proteomics applied to Erythropoiesis
Company: Lund University
Location: Lund, Sweden

Summary of position:
An exciting opportunity for a Postdoctoral Fellow is available immediately in the Proteomic Hematology group of Dr. Jenny Hansson at the Division of Molecular Hematology of the Lund Stem Cell Center, Lund University, Sweden. The Lund Stem Cell Center is a strategic center of excellence in life science, with a strong international position in the area of blood stem cell biology. We are seeking a highly motivated and ambitious postdoctoral fellow with a strong background in mass spectrometry-based proteomics to join a cross-disciplinary research project together with the research groups of Martin L. Olsson (MD, PhD, Prof.), Johan Flygare (MD, PhD) and Kenichi Miharada (PhD).

Description
The postdoctoral fellow will use cutting-edge mass-spectrometry based proteomics approaches to identify the regulators active in the erythropoietic niches. This includes the implementation and application of innovative sensitive mass spectrometry approaches for analysis of few primary cells obtained by micromanipulation (proximity-based single cell approach) and FACS. The postdoctoral fellow will be a critical part of a team working to establish novel concepts for how and where red blood cell production is controlled, ultimately providing promising targets for conceptually new pharmaceutical approaches to treat anemia, one of the most common medical conditions globally.

Qualifications required
Candidates are expected to have a strong background in mass spectrometry-based proteomics and knowledge in quantitative proteomics. Experience with both data-dependent and data-independent acquisition approaches is desirable but not essential. Knowledge in cell biology, especially hematopoiesis and erythropoiesis, is an advantage. Candidates must be highly motivated to pursue postdoctoral studies within proteomics methods development as well as to apply these methods to answer complex biological questions. Abilities to work independently as well as part of a team are essential. Excellent verbal and written communication skills in English are required for consideration. PhD degree should not be more than three years old at the last day of applying.

Application
Application stating the reference number V 2019/357 and containing a personal letter, CV including list of publications and names and contact information of at least two reference persons, should be sent to: Jenny.Hansson@med.lu.se.

Application deadline: 2019-09-05.

Link to full description: https://academicpositions.com/ad/lund-university/2019/postdoc-advanced-proteomics-applied-to-erythropoiesis/131676

Contact information: jenny.hansson@med.lu.se

Expression of Interest

Postdoctoral Research Fellow, Mass spectrometry-based proteomics

The Signalling Network Laboratory in the Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Australia aims to identify novel therapeutic targets and biomarkers for particular poor prognosis human cancers, including triple negative breast cancer, prostate and gastric cancer, through an integrated strategy that combines mass spectrometry-based proteomics with bioinformatics, computational biology and functional genomics.

Expressions of Interest are invited for a Postdoctoral Research Fellow position that will utilize mass spectrometry-based phosphoproteomic and kinomic profiling workflows and associated bioinformatic approaches to characterize cancer signalling networks, with the goal of identifying novel therapeutic targets and biomarkers. It will involve use of established workflows, as well as development of novel ones for interrogation of non-canonical phosphorylation events, and analysis of patient specimens. The fellow will also contribute to the functional characterization of lead candidates emanating from these studies.

Established expertise in mass spectrometry-based (phospho)proteomics is essential, with the ability to analyse large datasets using appropriate bioinformatics techniques desirable. Knowledge and experience in cell biology and signalling is also desirable.

For more information contact Professor Roger Daly, roger.daly@monash.edu

The Monash Biomedicine Discovery Institute (BDI) is one of the largest and most dynamic biomedical research and teaching environments in Australia. The Institute and its cognate Departments of Anatomy and Developmental Biology, Biochemistry and Molecular Biology, Microbiology, Pharmacology and Physiology comprise over 120 research groups. The BDI works closely with clinical and drug development precincts at Monash and has several major industry partnerships to facilitate the translation of their research. For more information about the BDI please visit their website at www.monash.edu.au/discovery-institute.