Intermediate files are generated and stored in your project folder at multiple processing steps. These files can be downloaded and opened for use in other tools or for applying to other types of analyses. View the community post on how to download files from either SCIEX Data Store or from BaseSpace.

An overview of some of the files created is given below.

After Extractor is run, a number of file types are created for each SWATH acquisition file processed:

• *.qresult – this file can be downloaded and opened in CloudConnect on the computer desktop if a user wants to visualize the processed results and see the peptide or metabolite XICs.
• *.cal.qresult – this file can be downloaded and opened in CloudConnect on the computer desktop if a user wants to visualize the processed retention time calibration results and see the RT Cal peptide XICs. This file is only present for proteomics workflows.
• *.qresult.export – this file contains several text files:

• *.qresult.export.cal – this file contains a number of different files pertaining to retention time calibration, listed below. Specifically, it contains the ForwardPeptideResults.txt file which can be used for checking the quality of the retention time calibration for that particular SWATH Acquisition file. In the OneOmics™ Suite, calibration is performed using the RT calibration peptides with a score above the median score, after exclusion of any outliers. This file is only present for proteomics workflows.

• Full_ion_library.txt – this file is an export of the final ion library built after library merging, with RT-Cal peptides included. This file is only present for proteomics workflows.

After Assembler is run, a number of files types are created. The results are filtered down to just the peptides or metabolites that had an FDR value of £1% in at least 1 sample in the study.

• FoldChange[denom].csv – this file provides easy access to the main quantitative results for the study.
  • This is a .csv file created for each experimental group in the study as the denominator, as noted in the square brackets. In this file is a list of proteins or metabolites and their fold change (fc), confidence (c) and p-value (p) for each comparison to the selected denominator in the study.

• • As an example, this file can be directly uploaded to iPathwayGuide (Advaita) for use in their pathway mapping toolkit for proteomics results.
• *[denom].fcresult – the file extension can be changed to .zip so that this file can be unzipped to extract many different results files, including the following files:

 

 

RUO-MKT-18-12201-A