TIC doesn't give you the information you need to sequence (Identify the protein), you need the spectral data from the peaks selected for the MS2 scan (and the parent masses of these spectra from the MS1 scan) to do that. 

You are performing bottom up proteomics as your proteins are digested. The chromatography is performed once and the mass spectrometer is continuously scanning what comes into the ESI source. At first it measure the MS1 spectra which contains multiple ions corresponding intact peptides. Then, the mass spectrometer select a given precursor ion and fragments it. the MS2 spectra correspond to this fragmentation. Usually the fragmentation energy allows for fragmentation betwen the amino acid residues and using tools such as proteome discover, mascot, sequest or MSGF+ you are able to interogate a database containing the sequence of proteins that could be present in your sample. Then you need to use a strategy for quantification area under peak, spectral count, ...

@ Luke V Schneiderr and Geremy Clair

Thank you for providing answers to my question.

Does it implies that I should have a single MS1 spectrum  and several MS2 spectra corresponding to different selected parent ions?

Also, can you be elaborate a little on the use of MS/MS for polypeptide sequencing?

For example, in the analysis of the data generated from my protein LC-MS/MS using Proteome Discoverer 2.1. and database search by Mascot and Sequest HT, a number of proteins having different percentage coverage and PSM (peptide spectrum match) were identified.

1. Will I combine the sequence of the various peptides identify for different proteins to predict my protein sequence?

2. Is the result only sufficient to identify closely related protein(s) and not sequence?-

3. If I am able to predict the sequence, how easy is it to get the N-terminal sequence?

Each MS2 spectra should be of a different parent peptide.  The parent peptide is fragmented (e.g., CID, ECD, PD, etc) into various pieces that constitute the peaks in the MS2 spectrum.  The cleavages of the parent peptide occur in specific ways many of which have been elaborated by Biemann (Methods in Enzymology).  There are also programs that will automatically read these spectra and interpret what parent is most likely to have generated that particular MS2 fragmentation pattern (e.g., MASCOT, PEAKS, Lutefisk, etc).  The fragmentation pattern can be interpreted manually, but this takes practice.  Once you have the sequence of the parent peptide from the MS2 spectrum, it is possible to identify the protein from which that peptide was derived by searching for a matching sequence in the protein sequence databases. 

Dear Sir,

We done our ESI-MS of our novel recombinant protein sample and found varying color (green,red,yellow) of peptide when matching to our known protein sequence (isolated and purified from plant source its ms spectra have identified 7 peptide and expressed it recombinantly). I have found all the peptide matching in our ESI-MS of recombinant protein with native protein ms (out of 7 peptide we have found 3 green 1 yellow and 3 red peptide). please clarify should i consider it my recombinant protein is have same sequence as native plant protein. Secondly what could be the reason of getting varying colour peptide.

Please clarify the significant of peptide deduced in sequence represented with varying color like green,Red and yellow. Could you please elaborate the percentage of similarity level of green, yellow and green peptides????

Thanks

Regards