Yes and no, depends on what kind of mass spectrometry, MS instrument brand, and what type of data. Assuming LC-MS/MS, there are several open-source programs that can interrogate the data against a protein database such as MaxQuant/Andromeda (https://www.maxquant.org/maxquant). The MS vendors typically provide proprietary software package as part of instrument purchase deal, so depending on the brand/model you may already have the software for protein analysis. More details about your experiment are needed to give specific recommendations.

Elena V Romanova Thanks for responding. I am working on mass spectrometry from Agilent technologies and we have the software Qualitative Masshunter provided by the company. This software gives us the mass spectrum and the deconvoluted mass expected. My question is: if I have a deconvoluted mass that is different from my protein, is there any possibility to know which is this protein without having a previous idea of what it could be?

Hiba Salim as I mentioned earlier, it is helpful to know what type of data you are receiving: is it deconvoluted mass of the molecular ion or fragment ions? If all you have from the measurement is molecular ion mass, then identifying this protein reliably will not be possible. There is, however, an option of checking for PTM from mass difference between predicted mass of the protein of interest and experimentally detected mass. Likewise, checking for protein degradation is possible by comparing detected mass against predicted fragmentation series. Good luck!

Dear Hiba,

As you are using an Agilent Tof or QTof LC/MS system, you can apply the Spectrum Mill SW package from the Broad Institute. You need to provide following information:

To get the latest version of Spectrum Mill:

Send an email message to [email protected] with your:

• Name
• Organization
• Email Address
• Phone Number

A Broad Institute representative will reply with a link to a download site to get the installation package.

There is also a demoversion available, just check out:

https://proteomics.broadinstitute.org

Spectrum Mill allows de-novo sequencing of unknown proteins, and the SW package is free of charge, but to get full access, you need to register at Broad Institute. Good luck!

Elena V Romanova Thank you a lot.

Holger Stalz Thank you a lot for recommending me the software. I have already registered and sent the email.