2. Introduction

Navigation through the webpage can be done by clicking on any of the four tabs at the left.

3. Input data

User can upload data using “Browse” buttons in “Variant Peptide Table” and “Genotype Data” menus. The format of both files can be found in section 2.3.

• The cloud-based SMAP application accepts .vcf files with meta-information (including none).

• Variant peptide data will be converted into log2 scale.

4. Data summary & filtering

For both variant peptide and genotype data, SMAP provides summary values and relevant distributions for the input files.

• Large genotype files may take a few moments to load

Variant peptide data summary (Example)

Genotype data summary (Example)

Users have the options to set each variant peptide filtering parameter (minimal intensity, maximal intensity, signal/noise ratio) and the genotype filtering parameter (number of missing genotypes tolerated per SNP) based on the data distributions.

Default parameters are set (and selected if no user input is given) as follows:

• Minimal and maximal intensity filters are set based on the means and standard deviations of the minimal and maximal peptide distributions.

• Signal/noise ratio is always set at the default of 3.

• Number of missing genotypes tolerated filter is OFF at default, but the user can set this filter if they have a large amount of missing data.

5. Run SMAP

After selecting the desired filters, SMAP is ready to run by clicking the “Run SMAP” button.

After running SMAP, an output table will be generated, which includes the variant peptide sample IDs and their matched genotype IDs. The Cscore and Delta Cscore for each match are also reported and graphed.

Users can download the result table by entering a file name and clicking download at the bottom: