A mass spectrometry template that adapts to your lab's workflow.
This mass spectrometry template ships with a 10-step protocol covering protein extraction through differential abundance analysis, validated TMT labeling and digest references, pre-wired instrument and search-engine parameters, and structured inputs for sample loading, fractionation, LC gradient, MS acquisition mode, search database, and result filtering thresholds. Your lab edits the configuration to match your samples and instrument, instead of restating the method from scratch every run.
See exactly how the template loads in ELabELN.
This is the live ELabELN experiment view, the same screen your lab works in every day. Switch between a blank start and a fully populated example, then expand any section to see what the template pre-fills.
What this mass spectrometry template ships with.
This mass spectrometry template ships configured for a bottom-up TMT 10-plex proteomics study on cultured cell lysates, with a 10-step protocol covering protein extraction through MaxQuant search, normalization, and differential abundance analysis. The protocol assumes a Thermo Q Exactive HF-X Orbitrap mass spectrometer, TMT 10-plex isobaric labeling, trypsin in-solution digest, high-pH reverse-phase offline fractionation, online nano-LC separation on a 25 cm C18 column, and HCD fragmentation at NCE 32%. Ten samples are pooled, fractionated into 12 fractions, and each fraction is analyzed in a separate 90-minute LC-MS/MS run.
Structured fields capture sample, labeling, and acquisition metadata in typed inputs (sample group, TMT channel assignment, protein input amount, digest enzyme and ratio, fractionation method, LC gradient, instrument and resolution settings, search engine and database, FDR threshold), so labeling schemes and acquisition parameters are queryable across studies instead of buried in free text. TMT reagents, trypsin lots, columns, and reference samples link to the ELabELN inventory so reagent and column-life traceability flow into every run record without manual entry. The spreadsheet editor captures the TMT labeling scheme (channel to sample) plus a top differentially abundant proteins (DAPs) summary table from the downstream Perseus analysis.
The template is intended as a tested baseline for academic and biotechnology research labs running quantitative proteomics, post-translational modification mapping, biomarker discovery, or protein-interaction studies. Configure the labeling scheme (label-free, SILAC, TMT-6plex, TMT-16plex, TMT-Pro), swap the instrument or acquisition mode (DDA, DIA), change the search engine (MaxQuant, FragPipe, Proteome Discoverer, Sage), or move from bottom-up to top-down by editing the digest and search sections. ELabELN's tamper-evident audit trail captures every labeling scheme, every search parameter set, and every analysis run, so the resulting record supports cross-cohort reproducibility documentation, multi-PI collaboration on shared proteomic resources, and FDA 21 CFR Part 11 review when the lab's quality system requires it.
Every ELN section, pre-populated for mass spectrometry.
The template populates the existing ELabELN sections your lab already works with: Main Text, Extra Fields, Steps, Compounds, Links, and more. Your team edits instead of building from scratch.
Main Text
Study design summary, instrument method notes, and expected ID depth, written in the TinyMCE editor.
- Hypothesis + design scaffold
- Instrument method version
- Linked to upstream lysate prep
Extra Fields
Twelve structured, typed fields grouped by Sample, Labeling, and Acquisition.
- Channel, group, protein input
- Digest, fractionation, LC, MS
- Queryable across cohorts
Steps
Ten-step workflow checklist covering lysis through MaxQuant search and Perseus differential analysis.
- Lyse, digest, label, mix
- Each tick timestamped
- Instrument run auto-logged
Compounds
TMT reagents, trypsin, column, mobile phase, and reference protein digests pre-linked from the compound database.
- TMT lot inline with channel
- Column-life tracking
- Low-stock warnings before run
Links & Resources
Pre-wired to your lab's MS SOPs, instrument method file, search database, and Perseus workflow.
- TMT 10plex SOP v2.1
- UniProt human reference
- Perseus workflow linked
Storage & Files
Labeled peptide aliquots, raw .raw files, peptide.txt and proteinGroups.txt output, and Perseus session files.
- -80 °C labeled peptide storage
- Attachment slots labelled
- TXT + Perseus ready on save
Use this template for your next proteomics cohort.
Edit the configuration to match your labeling scheme and instrument, run the cohort from a tested baseline, and capture every labeling table, instrument method, and analysis run in a structured record. Browse other templates built for the workflows real labs actually use.
Common questions
Can I configure the template for my labeling scheme and instrument?
Yes. Every section is editable. Swap in different labeling schemes (label-free, SILAC, TMT-6plex, TMT-10plex, TMT-16plex, TMT-Pro), change the instrument (Q Exactive, Orbitrap Exploris, Orbitrap Astral, timsTOF Pro, timsTOF SCP, Stellar), adjust the acquisition mode (DDA, DIA, BoxCar, PRM, SureQuant), or change the search engine and database. Save your edits as a private template scoped to your lab, or publish back to the ELabELN template library.
Does the template work for metabolomics or lipidomics too?
This template is configured for bottom-up proteomics. The structural pattern (sample prep, LC method, MS acquisition, identification, quantification) carries over to metabolomics and lipidomics, but the specific fields, library reference (HMDB, LipidMaps), and analysis tools (MS-DIAL, XCMS, MetaboAnalyst, LipidSearch) are different enough that a dedicated metabolomics template is more useful. The ELabELN team can scaffold a small-molecule MS variant during onboarding.
How does the template handle TMT ratio compression?
TMT ratio compression (the well-known underestimation of fold changes due to co-isolated interfering precursors) is a known issue with TMT quantification. The template captures whether SPS-MS3 quantification was used or whether ratio compression correction was applied at the analysis level (e.g., via Perseus or MS-EmpiRe). The structured field for this means downstream interpretation of fold change values has appropriate caveats documented in the experiment record.
Is it included in every ELabELN plan?
Yes. Every published template in the ELabELN library is available to all ELabELN subscribers in both Standard and Suite editions, with unlimited users in either edition.
Can my whole lab use this template?
Yes. Every ELabELN edition includes unlimited users, so the PI, sample-prep postdocs, MS facility staff, computational analysts, and rotating collaborators can all use the template without per-seat charges. Granular permissions let the PI control who can edit sample prep versus instrument method versus search parameters.
How quickly can my lab start running proteomics in ELabELN?
ELabELN Standard cloud deployment is typically live in 1-2 days. Once the instance is provisioned, this template loads from the library in a single click, with the labeling scheme, instrument method, and analysis pipeline editable to match the proteomics workflows your lab actually runs.