SeraDeg: Sera Degradation

SeraDeg
Serum Degradation Analysis
Build August 10, 2017.

Upload data - Analyse data
Upload and Analyse together

SeraDeg at once: Upload file and perform analysis

For repeated analysis of the same data, we suggest you to upload the spectra file separately. It will remain available for six months.
Go to the upload page first and then to the analysis interface later.

NB! Move your mouse over the icon Contextual help icon for a contextual help. Should you have any problem, see the help page.

Job information

Reference name for your analysis, you may change and adapt it to your needs. It is included within the name of result files. Job name:

If you provide a valid email address, results will be sent by email Your email:

Your country, for information and statistics only Country:

Input data

You must select a properly formatted archive file from your computer. This file must be uploaded to the server but it is removed as soon as it is used. Archive file:
(see example file In order to analyse the example file without downloading it first, go to the 'Analyse' form and input the following data:
Reference name: seradeg_example_file;
Your email: your actual email address;
File name: testAControls.zip )

The name of a reference spectrum, if available. By default, it's the spectrum whith the highest total abundance of fpA peptides.
The quality of all spectra is defined in comparison to this one. Reference spectrum name:

A standard signal may be added to sera before spectrometry for normalization aims. Select this option if your experiment included this component and you want to normalize data. You must also specify the corresponding m/z value. Normalization peak: No    Yes, at m/z

Advanced parameters Click 'Show' to show and revise advanced parameters.
Click 'Hide' to hide them. Show    Hide

The parameters for the median filter used to detect significannt peaks. Median filter parameters: Half window size:     Signal/noise ratio:

The thresholds to be applied on the total fpA peptide abundance for the assignment of quality score colors. Values are percent of the reference spectrum total fpA peptide abundance. Total abundance thresholds: Lower:%     Upper:%

Higher mass peptides thresholds: Lower:%     Middle:%     Upper:%

For information, get in touch with:
Paolo Romano,
Mass Spectrometry and Proteomics,
IRCCS Ospedale Policlinico San Martino,
Email: paolo.romano@hsanmartino.it

If you use SeraDeg, please cite the following paper:
Romano P, Beitia San Vicente M, Profumo A.
A mass spectrometry based method and a software tool to assess degradation status of serum samples to be used in proteomics for biomarker discovery.
Journal of Proteomics. Volume 173, 2018, Pages 99-106.
PMID: 29242081; DOI: 10.1016/j.jprot.2017.12.004