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      2. Getting started

      What types of experiments can MD 1.0 process?

      Our Generic Format means we can accept any kind of tabular data. We also support raw data based on Data Dependant Acquisition (DDA) and Data Independent Acquisition (DIA) experiments. Read on for more information.


      The below outlines the current support we offer. We continue to add further support, and welcome feedback based on what the community needs.

      Generic Format

      Choose this option if you have a tab-delimited table of intensities (before log transformation) quantified for several runs obtained using any software of choice. 

      This upload format was developed for protein level data. While any table with quantified features can be uploaded for quality control and differential expression, services like enrichment may not be available. 

      You can read more information in our Tech Note here.

      We support:

      • A minimum of 2 conditions, 3 replicates per condition

      Currently not supported:

      • Direct upload of output from any software 

      MaxQuant


      Choose this option if you have used MaxQuant to preprocess your raw data. We support unfractionated TMT (protein only) and LFQ data-dependent acquisition (DDA) experiments.  

      We support:

      • A minimum of 2 conditions, 3 replicates per condition

      Currently not supported:

      • Analysis of fractionated samples
      • SILAC, iTRAQ, Di-Methyl
      • DIA datasets processed using MaxDIA

      DIA Raw

      Choose this option if you have Thermo *.raw data-independent acquisition (DIA) data. 

      We support:

      • A minimum of 2 conditions, 3 MS raw data files per condition
      • Library-free processing
      • Use of a FASTA database 
      • Spectral library generation from DIA data

      Currently not supported:

      • Raw data beyond Thermo *.raw
      • Combined DDA and DIA data
      • Spectral library generation from DDA data
      • Upload of existing spectral libraries
      • Ability to define new post-translational modifications (PTMs)

      DDA Raw

      Choose this option if you have Thermo *.raw data-dependent acquisition (DDA) data. 

      We support:

      • Data generated with Trypsin protein digestion
      • A minimum of 2 conditions, 3 MS raw data files per condition
      • Use a FASTA database that contains reviewed proteins

      Currently not supported:

      • Raw data beyond Thermo *.raw
      • Fractionated samples
      • Combined DDA and DIA data
      • Ability to define new post-translational modifications