Absolute expression format

The absolute expression format aims to cover the following use cases:

  • Fast and easy visualization absolute expression (AE) results using iBAQ values.

  • Store the AE results of each protein on each sample.

  • Provide information about the condition (factor value) of each sample for easy integration.

  • Store metadata information about the project, the workflow and the columns in the file.

Format

The absolute expression format by quantms is a tab-delimited file format that contains the following fields:

  • protein -> Protein accession or semicolon-separated list of accessions for indistinguishable groups

  • sample_accession -> Sample accession in the SDRF.

  • condition -> Condition name

  • ibaq -> iBAQ value

  • ribaq -> Relative iBAQ value

Example:

protein

sample_accession

condition

ibaq

ribaq

LV861_HUMAN

Sample-1

heart

1234.1

12.34

AE Header

By default, the MSstats format does not have any header of metadata. We suggest adding a header to the output for better understanding of the file. By default, MSstats allows comments in the file if the line starts with #. The quantms output will start with some key value pairs that describe the project, the workflow and also the columns in the file. For example:

#project_accession=PXD000000

In addition, for each Default column of the matrix the following information should be added:

#INFO=<ID=protein, Number=inf, Type=String, Description="Protein Accession">
#INFO=<ID=sample_accession, Number=1, Type=String, Description="Sample Accession in the SDRF">
#INFO=<ID=condition, Number=1, Type=String, Description="Value of the factor value">
#INFO=<ID=ibaq, Number=1, Type=Float, Description="Intensity based absolute quantification">
#INFO=<ID=ribaq, Number=1, Type=Float, Description="relative iBAQ">

  • The ID is the column name in the matrix, the Number is the number of values in the column (separated by ;), the Type is the type of the values in the column and the Description is a description of the column. The number of values in the column can go from 1 to inf (infinity).

  • Protein groups are written as a list of protein accessions separated by ; (e.g. P12345;P12346)

We suggest including the following properties in the header:

  • project_accession: The project accession in PRIDE Archive

  • project_title: The project title in PRIDE Archive

  • project_description: The project description in PRIDE Archive

  • quanmts_version: The version of the quantms workflow used to generate the file

  • factor_value: The factor values used in the analysis (e.g. tissue)

Please check also the differential expression example for more information Differential expression format