1. Sample list template

Download the sample template using the download button in the upper left corner of the app.

Open the Excel template and edit the form.

table column explanation
sample name of your sample
protein concentration (µg/µl) determined protein concentration of sample
OT-2 slot OT-2 slot were the sample is standing (max N = 4)
OT-2 position OT-2 position inside the slot (max N = 24)
volume sample volume inside the sample tube (essential for liquid height function)
preparation plate position the position in the preparation plate (leave as it is !)

IF YOU DO NOT SPECIFY THE SAMPLE NAME ALL OTHER INFORMATION IN THE ROWS ARE NEGLECTED !

Sample volume

Sample volume is set by the user in the table. However, all volumes below 60µl were taken out with 0.5mm distance from the bottom.

2. Parameters

Just select the desired parameters like enzyme:protein ratio etc.

ADVICE: Use the calculated concentrations since they are optimized for adding always 2µl of enzyme to the sample !

3. Processing and Download

After processing you can download the OT-2 protocols and decklayouts etc.

The downloaded zip-folder contains the decklayout plots and the python scripts for the OT-2.

The Interfaculty Institute for Genetics and Functional Genome Research is responsible for the content of this website.

Information on data protection

The responsible body within the meaning of the General Data Protection Regulation and other national data protection laws of the member states as well as other data protection regulations is:

Greifswald University Medical Center
Corporation under public law
Interfaculty Institute for Genetics and Functional Genome Research
Dr. Stephan Michalik
Felix-Hausdorff-Strasse 8
17475 Greifswald
Phone +49 3834 420 5821
E-mail Stephan.michalik@uni-greifswald.de

Data Protection Officer
Prof. Ulf Glende
Group Data Protection Officer at UMG
Walther-Rathenau-Strasse 49
17475 Greifswald
Phone +49 3834 6194
datenschutz-umg@med.uni-greifswald.de

Data collection when you visit our website

When you use our website, we only collect data that your browser transmits to our server (“server log files”). When you visit our website, we collect the following data, which is technically necessary for us to be able to display the website to you:

  • Date and time at the time of access
  • No uploaded data is stored on the server after closing the session. The data processing is carried out in accordance with Art. 5 (1) point of the GDPR on the basis of our legitimate interest in improving the stability and functionality of our website. The data will not be passed on or used in any other way.

The data protection guidelines of University Medicine Greifswald (UMG) apply. Data protection declaration according to Art. 13 DSGVO applies. (https://www.medizin.uni-greifswald.de/de/service/datenschutz/)

Use of the app

Do not use clinical or personalized data where an individual can be traced. Use of the app and the files it generates is without any guarantee.

Version 1.1.1

  • add additional error messages for the digest module, when the provided sample table have missing values in volume or protein concentration column

Version 1.1.0

  • BCA assay: addition of take3 BCA assay for low sample volumes
    • using max. 50µl and min. 25µl as total dilution volume
    • allowing dilution up to 50 fold
    • sample volume for dilution is calculated in balance (e.g. 5 µl in 25µl total volume = 5 fold dilution / 2 µl in 50 µl total volume = 25 fold dilution)
  • BCA assay: adding hard coded standard curve in the analysis for a better comparison of the measurement
  • BCA assay: show error when sample volume left after dilution is to low; also hide download bar in that case
  • BCA assay: adding the sample volume and buffer volumes to the html file for a more comprehensive documentation
  • BCA assay: adding pipetting quality to the table for a better anticipation of the pipetting accuracy and precision
  • digest: loading Evotip now include touch tip command during the distributions to avoid droplet carryover during washing step

Version 1.0.0

  • initial release
  • described in: Reder, A., Hentschker, C., Steil, L., Gesell Salazar, M., Hammer, E., Dhople, V. M., Sura, T., Lissner, U., Wolfgramm, H., Dittmar, D., Harms, M., Surmann, K., Völker, U., & Michalik, S. (2023). MassSpecPreppy—An end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications. Proteomics, 00, e2300294. https://doi.org/10.1002/pmic.202300294

usage

The usage of the app is fairly simple. Just download the excel template for your sample description (sample name, dilution factor, replicate). The edited excel table can then be uploaded together with the excel file output from the Gen5 software (Synergy H1 plate reader).

DO NOT USE “STD” or “BLK” in sample naming !!!.

96 well plate measurements

The 96well plate can be measured in “normal” read mode in the Synergy H1 as well.

Please download the Excel template from the app to provide the meta data of your samples to the app.

comment column in output

The app will export all relevant data and the samples will get a comment field. Please make sure that your dilution of samples is measured in the acceptable (“OK”) range.

The Interfaculty Institute for Genetics and Functional Genome Research is responsible for the content of this website.

Information on data protection

The responsible body within the meaning of the General Data Protection Regulation and other national data protection laws of the member states as well as other data protection regulations is:

Greifswald University Medical Center
Corporation under public law
Interfaculty Institute for Genetics and Functional Genome Research
Dr. Stephan Michalik
Felix-Hausdorff-Strasse 8
17475 Greifswald
Phone +49 3834 420 5821
E-mail Stephan.michalik@uni-greifswald.de

Data Protection Officer
Prof. Ulf Glende
Group Data Protection Officer at UMG
Walther-Rathenau-Strasse 49
17475 Greifswald
Phone +49 3834 6194
datenschutz-umg@med.uni-greifswald.de

Data collection when you visit our website

When you use our website, we only collect data that your browser transmits to our server (“server log files”). When you visit our website, we collect the following data, which is technically necessary for us to be able to display the website to you:

  • Date and time at the time of access
  • No uploaded data is stored on the server after closing the session. The data processing is carried out in accordance with Art. 5 (1) point of the GDPR on the basis of our legitimate interest in improving the stability and functionality of our website. The data will not be passed on or used in any other way.

The data protection guidelines of University Medicine Greifswald (UMG) apply. Data protection declaration according to Art. 13 DSGVO applies. (https://www.medizin.uni-greifswald.de/de/service/datenschutz/)

Use of the app

Do not use clinical or personalized data where an individual can be traced. Use of the app and the files it generates is without any guarantee.

Version 1.1.1

  • add additional error messages for the digest module, when the provided sample table have missing values in volume or protein concentration column

Version 1.1.0

  • BCA assay: addition of take3 BCA assay for low sample volumes
    • using max. 50µl and min. 25µl as total dilution volume
    • allowing dilution up to 50 fold
    • sample volume for dilution is calculated in balance (e.g. 5 µl in 25µl total volume = 5 fold dilution / 2 µl in 50 µl total volume = 25 fold dilution)
  • BCA assay: adding hard coded standard curve in the analysis for a better comparison of the measurement
  • BCA assay: show error when sample volume left after dilution is to low; also hide download bar in that case
  • BCA assay: adding the sample volume and buffer volumes to the html file for a more comprehensive documentation
  • BCA assay: adding pipetting quality to the table for a better anticipation of the pipetting accuracy and precision
  • digest: loading Evotip now include touch tip command during the distributions to avoid droplet carryover during washing step

Version 1.0.0

  • initial release
  • described in: Reder, A., Hentschker, C., Steil, L., Gesell Salazar, M., Hammer, E., Dhople, V. M., Sura, T., Lissner, U., Wolfgramm, H., Dittmar, D., Harms, M., Surmann, K., Völker, U., & Michalik, S. (2023). MassSpecPreppy—An end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications. Proteomics, 00, e2300294. https://doi.org/10.1002/pmic.202300294