School of Bioinformatics · Systems & multi-omics
Proteomics & Metabolomics Data Analysis
Mass spectrometry measures the proteins and small molecules that carry out cellular functions. This course teaches how spectra become identifications and quantities, and how to test and interpret differences between conditions.
Course overview
Proteomics & Metabolomics Data Analysis covers the computational side of mass-spectrometry experiments: database search and false discovery rates, label-free and isobaric quantification, missing values, normalisation and statistical testing.
The metabolomics half covers peak detection and alignment, annotation confidence levels and pathway analysis, and the course closes with a practical comparison of the two data types and how to integrate them with transcriptomics.
Learning outcomes
By the end of the course you will be able to:
- Explain how peptides are identified from spectra and how FDR is controlled
- Quantify proteins with label-free and TMT approaches
- Handle missing values, normalise and test differential abundance
- Process untargeted metabolomics data and report annotation confidence
- Interpret results with pathway and network analysis
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- R for Bioinformatics or equivalent
- Basic biochemistry
Best suited to
- Researchers using proteomics or metabolomics core facilities
- Biochemists and pharmacologists with MS data
- Bioinformaticians extending into multi-omics
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- LC-MS/MS, DDA and DIA
- Spectra, precursors and fragments
- Experimental design
Topics
- Database search
- Target–decoy FDR
- Protein inference
Topics
- Label-free and TMT
- Normalisation and missing values
- MSstats and limma
Topics
- Peak picking and alignment
- Annotation and confidence levels
- Statistics and pathway analysis
Topics
- Matching identifiers across omics
- Joint pathway analysis
- Correlation networks
Topics
- Analysis
- Interpretation
- Reporting standards
Practical sessions and projects
Capstone project
Report an MS study
Analyse a public proteomics or metabolomics dataset from identification to pathways and report it with the metadata and confidence levels that reviewers expect.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- Mass spectrometry for analysts
Open raw spectra, inspect precursor and fragment scans and match a peptide by hand.
- Identification
Search a public dataset with FragPipe and examine how the FDR threshold changes the protein list.
- Quantification and statistics
Find differentially abundant proteins between two conditions and visualise them.
- Metabolomics
Process an untargeted metabolomics dataset and report annotated, significant metabolites with their confidence level.
- Integration
Combine protein, metabolite and transcript changes in shared pathways.
- Project: a multi-omics result
Analyse a public proteomics or metabolomics study and report it to community standards.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- PRIDE proteomics datasets: Identification and quantification.PRIDE archive (public)
- MetaboLights studies: Metabolomics processing.EMBL-EBI MetaboLights (public)
Core reading
- Cox J, Mann M (2008). MaxQuant enables high peptide identification rates. Nature Biotechnology 26:1367–1372.
- Pang Z et al. (2021). MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights. Nucleic Acids Research 49:W388–W396.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Proteomics & Metabolomics Data Analysis, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Proteomics & Metabolomics Data Analysis
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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