Peptide mass fingerprinting is the way to identify the proteins and peptides like oxidation of methionine in proteins and peptides. Protein identification using PMF data is performed by comparing experimentally determined peptide masses of a protein cleaved by a specific protease to in silico generated PMFs of known protein sequences. Using R[ one can analyze the measurement error and calibrate the masses,  find contaminants and remove them,  submit peak-lists to the identification software Mascot, and analyse the search result. For this tasks we use functionality provided by R e.g.: spline functions (R/modreg), linear regression, functions for matrix computation, descriptive statistic functions (R/base) and clustering algorithms (R/mva). In addition we implemented functions for pairwise protein sequence comparison in the package R/pairseqsim and for communication with web servers in the package R/httpRequest. The m/z and intensity value pairs assigned to each peak in a spectrum

are stored along with the position of the sample on the MALDI sample support

in the Massvector object. With the help of mass spectrometers one can analyze

several hundred samples on a single sample support.

Thank you very much. Which kind of analysis is suitable for a biomarker discovery experiment?

Dear Sugandima Vidanagamachch,

in first, For your question i agree Ravi Kant Upadhyay sir answer, in addition to that some concern,

Only way for identifying exact protein is via mas spectrum by MALDI-TO-MS, ESI-MS-MS,

In your case also you have said same, yah you can able to identify protein by using peaklist in R, but before that you should have to know about same reference peptide analysis report, and if your protein is unknown means by appearing mass you some what possible to predict what is that, by using theoretical fragment method around 70%you can able to get confirm this but not possible 100%

You can able to list out the variations between m/z of reference and m/z of your out put peak data value and variations of m/z of peak measurements, then you can able to find clearly, if your protein is unknown means in the position of reference m/z, you can use theoretical fragment values.,

No need confusion in this by using direct MALDI-TOF-MS value just you check M+2H+ and M+4H+, if possible M+H+  from this directly you can identify the protein which you have and report out this, you want to make understand clearly to your viewers means you list our all the peaks as for you said.

If you need to understand position of each amino acids in your protein means go for amino acid sequences analyzer with the help of EMPOWER Software.

In-fact by looking MALDI-TOF we can just find the protein mass and predict the protein, we have analyzed variety of proteins and peptides and list outed. if any doubt write it back, 

For your second question, Biomarker means under which section?  in general for Biomarker discovery analysis : Evaluation of qPCR curve analysis methods was using. did you mean qualitative or quantitative methods?  anyway for this you just read articles from the "Biomarkers" Journal, it have verity of analysis details and specification.

Hope You Clear..,

Good Luck & Regard

R.Selva..........

Thanks a lot. I used Mascot tool for the identification of proteins.

http://www.waters.com/waters/en_GB/Empower-3-Chromatography-Data-Software/nav.htm?locale=en_GB&cid=10190669

Is this the software u referred? It seems not free.

I want to use quantitative methods for Biomarker discovery of a particular disease. I think I have to use the proteins identified by mascot tool for this.

Thanks.

Dear Sugandima,

In this case you will definitely need an ESI-MS/MS platform.

You can try using iTRAQ on MALDI but it'll be grossly relative  n you may need several repeats.

Best wishes,

Kaushiki

Thanks a lot,  I use the results of those experiments.