The NP tables summarize LFQ results at the individual nanoparticle level. In the Panel tables, the single quantification value for a particular peptide or protein group represents the quantitation value of the NP measured most frequently across all samples (Max Representation roll-up)

Analysis results can be exported by first selecting an analysis from the Analyses page, and then selecting the ‘Protein Group/Peptide Results’ button in the results tab. Results are exported as peptide and protein group .csv files.

Proteograph^® assay controls and their analysis results are tracked separately on the ‘QC Charts’ tab. From this page key performance metrics are automatically recorded and can be quickly reviewed relative to control results from other plates or studies. Statistical limits are calculated based on historical data and displayed to evaluate deviations from expected ranges.

From the Analyses page, select a completed analysis and then select the ‘Group Analysis’ tab to review the quantitation results organized in groups according to the sample metadata. From this page, select the ‘Setup Group Analysis’ button to access a guided wizard that will setup the differential expression analysis of specific samples or groups of samples.

The sample description file is an optional .csv file that a user may provide to indicate additional metadata (ie. condition, description, replicate, etc.). This file can be associated with a plate during plate addition or from the Plates page to an existing plate.

The plate map file is a .csv file that specifies the location of each sample and control in a 96-well plate. The instrument control software (ICS) generates the file and automatically populates each column except MS file name. You must specify the MS data file name in the first column of the file, and then upload it to PAS during analysis setup.

The Projects page offer two ways to start an analysis: Analyze and Analyze Controls. The Analyze button analyzes all selected samples in a project, including controls. The Analyze Controls button analyzes controls in the project only. Both buttons open a dialog where you can name the analysis, specify the analysis protocol, and input other general information.

To reanalyze data analyzed using the Proteograph^® Analysis Suite, go to the Projects page, select the samples you want to reanalyze, and select Analyze. This option is useful for reanalyzing data using a different analysis method.

The first step of setting up an analysis depends on preference: start either on the Plates page by selecting Add Plate or on the Data Files page by selecting Link to Plate. Alternatively, you can start on the Projects page and select existing samples.

Any mass spectrometer instrument designed for proteomic analysis can fit seamlessly into the Proteograph^® workflow. Upon request, Seer can provide recommended methods for LC-MS implementation.