ProteoSign is an online service for protein differential expression (or abundance) analysis designed with the end-proteomics user in mind.

Borrowing from the experience of the microarray field, ProteoSign software utilizes the well-established Linear Models For Microarray Data (LIMMA) methodology for assessing statistical significance in protein abundance differences between two or more proteome states.

ProteoSign aims to fully automate the process of statistically evaluating differential expression in mass spectrometry-based bottom-up (shotgun) quantitative proteomics data by requiring minimal user interaction time and generating publication-quality data plots.

Click Start to begin your analysis.

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Select one or more (by holding the Ctrl key).
Select a dataset and press OK.
You can also download it to your machine.
Select a condition to assign to the selected raw files
or type a New condition in the box below.

ProteoSign says:

Please type the Name of the New condition:
Label Swap Assignment
Please select the Biological and Technical replicate where labels were swapped
Raw files affected:
  Then, select the Labels that were swapped and click Add to assign the swap
Current label swaps assigned:
Change the default data analysis parameters used by ProteoSign and click OK
Proteins that were not qualified with at least different peptides in at least biological replicates will be disqualified.
Adjusted p-value threshold for differentially expressed proteins:
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Replication Multiplexing

ProteoSign supports data sets that have biological or technical replicates represented as different tags. Please choose the options below that best describe your experiment and click Next:
If you have no technical replicates select "Raw Files" as the corresponding option

My biological replicates are represented as different Raw Files Tags

My technical replicates are represented as different Raw Files Tags

My conditions are represented as different Raw Files Tags