Doctoral student in Probabilistic Modelling of Errors in Mass Spectrometry-Based Proteomics

Project description

Third-cycle subject: Biotechnology

This project aims to develop robust methods for assessing identification and quantification errors in shotgun proteomics. We will construct probabilistic models to characterize errors in peptide and protein identification from mass spectrometry data. Additionally, we will extend these models to quantify how identification errors propagate to protein-level quantification. By evaluating existing methods and proposing novel approaches, the project seeks to improve the reliability of proteomic data analysis, ultimately enhancing downstream biological interpretations.

The project will utilize improved probabilistic regression models to estimate identification and

quantification error rates in proteomics data. These error rates will be modeled using hierarchical Bayesian networks to capture dependencies between peptides and proteins. We will implement and test these models on benchmark datasets, comparing their performance against existing approaches.

Additionally, we will develop scalable computational tools to integrate these models into current proteomics workflows, ensuring practical applicability.

Supervision: Lukas Käll is proposed to supervise the doctoral student. Decisions are made on admission

Admission requirements

To be admitted to postgraduate education (Chapter 7, 39 § Swedish Higher Education Ordinance), the applicant must have basic eligibility in accordance with either of the following:

• Mobility rules - Candidates must not have resided or conducted their main activity (work, studies, etc.) in Sweden for more than 12 months in the 3 years immediately preceding the recruitment date,
• passed a second cycle degree (for example a master's degree), or
• completed course requirements of at least 240 higher education credits, of which at least 60 second-cycle higher education credits, or
• acquired, in some other way within or outside the country, substantially equivalent knowledge.

In addition to the above, there is also a mandatory requirement for English equivalent to English B/6.

Selection

In order to succeed as a doctoral student at KTH you need to be goal oriented and persevering in your work. During the selection process, candidates will be assessed upon their ability to:

• independently pursue his or her work
• collaborate with others,
• have a professional approach and
• analyze and work with complex issues.

We favor applicants with education in quantitative sciences, such as Physics or Computational Science.

After the qualification requirements, great emphasis will be placed on personal skills. 

Target degree: Doctoral degree 

Information regarding admission and employment

Only those admitted to postgraduate education may be employed as a doctoral student. The total length of employment may not be longer than what corresponds to full-time doctoral education in four years' time. An employed doctoral student can, to a limited extent (maximum 20%), perform certain tasks within their role, e.g. training and administration. A new position as a doctoral student is for a maximum of one year, and then the employment may be renewed for a maximum of two years at a time. 

As a doctoral student, you are entitled to a workplace with many employee benefits and monthly salary according to KTH’s Doctoral student salary agreement. Read more about Doctoral studies (PhD) | KTH | Sweden.

Allowances- In addition to the starting basic salary mentioned in above link, all positions within Marie Curie contains a mobility allowance and possible family allowance, for more information read here. Basic salary and supplementary allowances are specified pre tax.  

Union representatives

Contact information for union representatives.

Doctoral Student’s network (Students’ union on KTH Royal Institute of Technology)

Contact information for PhD chapter.

To apply for the position

Apply for the position and admission through KTH's recruitment system. It is the applicant’s responsibility to ensure that the application is complete in accordance with the instructions in the advertisement.

Applications must include the following elements:

• Copies of diplomas and grades from previous university studies and certificates of fulfilled language requirements (see above). Translations into English or Swedish if the original document is not issued in one of these languages.Copies of originals must be certified.
• CV including your relevant professional experience and knowledge.
• Application letter with a brief description of why you want to pursue research studies, about what your academic interests are and how they relate to your previous studies and future goals. (Maximum 2 pages long)
• Representative publications or technical reports. For longer documents, please provide a summary (abstract) and a web link to the full text.

Applications must be received at the last closing date at midnight, CET/CEST (Central European Time/Central European Summer Time).

Other information

For information about processing of personal data in the recruitment process.

It may be the case that a position at KTH is classified as a security-sensitive role in accordance with the Protective Security Act (2018:585). If this applies to the specific position, a security clearance will be conducted for the applicant in accordance with the same law with the applicant's consent. In such cases, a prerequisite for employment is that the applicant is approved following the security clearance.

We firmly decline all contact with staffing and recruitment agencies and job ad salespersons.

Disclaimer: In case of discrepancy between the Swedish original and the English translation of the job announcement, the Swedish version takes precedence.

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1. Lukas Käll, [email protected]