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Mon, 23 Oct 2017 11:19:45 UTC — Version 2.10  
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PeakInvestigator™ Direct Access Instructions

Veritomyx offers a user interface directly from your browser that allows you to upload and process mass spectrometry scans through the PeakInvestigator™ software services (PI Direct Access). Submitted scans must be in ASCII tab-delimited format, but multiple individual scans may be compressed within a .zip or .tar package for faster uploads. You must register and establish a valid user account with Veritomyx to use PI Direct Access.  Once you have completed Login at, you will have direct access to PeakInvestigator, where you can:

  1. Upload the scan file(s) to be processed, via either:
    • “Upload” hyperlink (maximum upload size 100MB)
    • SFTP utility (required for files over 100MB)
  2. Submit the scan(s) for PeakInvestigator processing.
  3. Monitor the status of job progress.
  4. Download the PeakInvestigator peak lists, for completed jobs.

1.  Upload File(s)

Raw (continuum or profile) MS file(s) can be uploaded directly to the PeakInvestigator servers to be staged for processing. The Import Interface Specification format requirements for your files to be uploaded can be found directly at:

If you wish to upload and process multiple individual scans, they may be compressed within a .zip or .tar package for faster uploads as a single file. Multiple scans submitted in a .zip or .tar format can only be processed together by PeakInvestigator as a single Job.

  • File Upload Facility (up to 100 MB).  Select the Upload link in the "Files & Jobs" section of your Project or SubProject page. This will take you to the File Upload Facility, where you can click on the Browse button to select an individual scan file to be submitted from your computer. Then click on the Upload button to begin transmission. When uploaded, the scan will appear in the Uploaded Files list. Note that uploading files via this web browser is limited to file uploads totaling less than 100MB.

  • SFTP Uploads (any size). An SFTP application such as FileZilla (a popular open source option) may be utilized. All of the server settings and credentials needed to correctly set up your SFTP upload are shown in the View API & SFTP Information link under Actions on your Project or SubProject page. If you encounter difficulties with the SFTP upload, carefully review your input settings and attempt it repeatedly, or you may need to access advanced settings for your SFTP application in order to input the necessary credentials.

    If you are planning large SFTP uploads (100 GB or more), we suggest coordinating with us in advance at, so that we may ensure sufficient disk space is available and dedicated for your uploads.

Once you have a scan file uploaded, you should then click on the Prep File link to have the system analyze it to complete consistency and acceptability checks in preparation for submitting it for processing. The Prep File process may a take several minutes or longer depending on the number and size of files being prepared. Remember to refresh your browser window to update the Prep File status after it has progressed into Analyzing status.

2.  Submit Job

Uploaded scans must now be submitted as Jobs to the PeakInvestigator software services. Find and select the Centroid link for your particular file.  This will take you to a Job Configuration page that identifies the scan(s) and assigns it a unique Job name.

PeakInvestigator software requires a minimum of 11 isolated (non-overlapped) peaks distributed over the m/z range designated for analysis, to facilitate proper operation. If the scan submitted for processing does not contain a sufficient number of peaks, you have the option of choosing any one of your uploaded files (a single .txt scan, or a .zip or .tar set of scans) as a "characterization file" that does contain enough isolated peaks for PeakInvestigator to process during Job Configuration. Note that if you submit multiple scans for processing in a .zip or .tar format, you cannot select a characterization scan from within the .zip or .tar group of scans. The characterization file must be obtained from the same instrument using the same tuning parameters as the scans to be processed by PeakInvestigator or performance may be adversely affected. Ideally, the characterization scan should immediately precede or follow the scans designated for analysis, with no intervening changes in settings on the mass analyzer.

Click on the Submit Job button to send the scan to PeakInvestigator for processing. After submission, you will be returned to the project page where you will see the Job number has been added to the Running Jobs queue and the recently submitted scan now shows a Locked to job status in the list of Uploaded Spectra.

3.  Monitor Status

You can monitor the status of Jobs submitted from your appropriate Project or SubProject page at any time. Click on the job number or refresh the page in your browser window to ensure that the job status has updated.

4.  Download Results

When the Job has completed, you may retrieve the PeakInvestigator peak list results for any completed Jobs by clicking the .mass_list.[filetype] file that appears as the Results file when viewing your job details. If a single *.txt file is processed, its results will carry the original scan name with a “.mass_list.txt” suffix.

If you uploaded a group of scans in a *.zip or *.tar format, the resulting peak lists will generally be compressed to carry the original scan name with a “.mass_list.[zip or tar] suffix.

Once downloaded and uncompressed, the peak lists will be in ASCII tab-delimited format.

When you download results through the web browser interface or as instructed within the API specifications, your job is promptly deleted from the PeakInvestigator servers. If you download results through the SFTP interface, and you fail to manually delete your job, it will nonetheless be deleted automatically within two weeks after the job is completed - so remember to save your results!

IMPORTANT NOTE: Remember to save your work after downloading PeakInvestigator results to your computer, as they are not retained or archived on the PeakInvestigator servers.

Note that it can take some time to process your job(s) depending on the size of the data file(s) and how busy the PeakInvestigator servers are at the time of submission. PeakInvestigator typically provides sufficient processing facilities to ensure job completion within one working day of job submission. You may logout of the website and log back in later to check on the status and to retrieve your completed jobs.

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