Mass Dynamics 1.0 provides the following statistical output tables for the analysis of uploaded MaxQuant data, or record keeping:

• peptides_quant.txt
• peptides_quant_intensities.txt
• proteinGroups_quant.txt
• proteinGroups_quant_intensities.txt
• modificationSpecificPeptides_quant.txt
• modificationSpecificPeptides_quant_intensities.txt

Output files are in wide format if ending with the prefix _quant.txt and in long format if ending with the prefix _quant_intensities.txt. Wide format tables are analogous to MaxQuant input tables but contain columns with limma result statistics whereas long format tables contain information pertaining to each measurement contained in the corresponding table.

For example, a proteinGroups.txt file will contain 8 intensity columns for a single protein group if there are 4 samples in each experimental group for an LFQ experiment. If 3 of these sample measurements are missing for a given protein, the quantification for that contrast will be calculated and the imputed values are contained within the long form table, proteinGroups_quant_intensities.txt.

Definitions of columns created by maxquant can be found in the maxquant documentation here: http://www.coxdocs.org/doku.php?id=maxquant:table:directory

Quantification Results in _quant.txt wide format output files are interpretable as per the limma R package² Documentation http://bioconductor.org/packages/devel/bioc/manuals/limma/man/limma.pdf

We reproduce the relevant text here for ease of access: (Note: that pairwise tests are performed and group combinations such as “A - B” are appended to column names to associate the relevant comparison to its statistics.)

• logFC: estimate of the log2-fold-change for one contrast There may be several columns of logFCs, one for each pairwise comparison.
• CI.L: left limit of the confidence interval for the logFC.
• CI.R: right limit of the confidence interval for the logFC.
• P.Value: raw p-value for the logFC.
• adj.P.Value: adjusted p-value or q-value for the logFC.

The following statistics are provided for an ANOVA test which considers all groups concurrently:

• AveExpr: average log2-expression for the feature (peptide or protein) across all samples.
• F: moderated F-statistic (omitted from topTable unless more than one coef is specified).
• adj.P.Value: adjusted p-value or q-value