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[0021] All percentages, ratios, and proportions used herein are by weight unless otherwise specified. 

[0022] As used herein, abbreviations will be used to describe amino acids. Such abbreviations are described in Table I below. Further described in Table I are average amino acid residue masses which are useful for the practice of the present invention. The residue mass of modified lysine will have to be appropriately adjusted following derivatiza› tion with natural abundance or heavy isotope enriched lysine-modification reagents. 

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[0023] As used herein, the term "desorption ionization" refers to the transition of an analyte from the solid-phase to the gas-phase as ions. 

[0024] As used herein, the term "desorption" refers to the departure of analyte from the surface and/or the entry of the analyte into a gaseous phase. 

[0025] As used herein, "ionization" refers to the process of creating or retaining on an analyte an electrical charge equal to plus or minus one or more electron units. 

[0026] As used herein, the term "MALDI" refers to matrix-assisted laser desorption ionization. 

[0027] As used herein, the term "matrix" in reference to "MALDI" refers to small, acidic, light absorbing chemicals which may be mixed in solution with the polypeptide of interest, or peptides thereof, of interest in such a manner so that, upon drying on the sample stage, the crystalline matrix› embedded analytes can be successfully desorbed and ionized from the solid-phase into the gaseous or vapor-phase fol› lowing laser irradiation. Alternatively, solutions of polypep› tides, or peptides thereof, may be loaded onto appropriate matrices which are pre-dried on the sample stage. Non› limiting examples of suitable matrices include nicotinic acid, sinapinic acid, ferulic acid, caffeic acid, a-cyano-4- hydroxycinnamic acid, and a-cyano-4-hydroxycinnamic acid mixed with nitrocellulose. 

[0028] As used herein, the term "electrospray ionization" refers to the process of producing ions from solution by 

## Definitions 

electrostatically spraying the solution from a capillary elec› trode at high voltage with respect to a grounded counter electrode. The definition is intended to include both elec› trospray ionization and pneumatically assisted electrospray ionization, which is also referred to as ionspray. As used herein, the term "electrospray ionization" applies to all liquid flow rates and is intended to include microspray and nanospray experiments. Moreover, the definition is intended to apply to the analyses of peptides directly infused into the ion source without separation, and to the analysis of peptides or peptide mixtures that are separated prior to electrospray ionization. Suitable on-line separation methods include, but are not limited to, HPLC, capillary HPLC and capillary electrophoresis. Electrospray ionization experiments can be carried out with a variety of mass analyzers, including but not limited to, triple quadrupoles, ion traps, orthogonal› acceleration time-of-flight analyzers and Fourier Transform Ion Cyclotron Resonance instruments. 

[0029] As used herein, the term "polypeptide" refers to a molecule having two or more amino acid residues. The method of the present invention is suitable for sequence identification of high mass polypeptides. 

[0030] As used herein, the term "wild-type" refers to a polypeptide produced by unnmtated organisms. 

[0031] As used herein, the term "variant" refers to a polypeptide having an amino acid sequence which differs from that of the wild-type polypeptide. As used herein, the term "very basic group" refers to a functional group with a pKa greater than 9 .5 including, but not limited to groups like guanidinium groups. 

[0032] As used herein, the term "fixed cationic-charged group" refers to a group comprising a permanent positive charge including, but not limited to functional groups such as a quaternary amine, sulfonium or pyridinium. 

[0033] As used herein, the term "isotopically labeled group" refers to a group comprising at least one atom that is enriched for an isotope that is higher or lower in molecular weight than the most common natural abundance isotope of the atom including, but not limited to groups such as $^{15}$N containing guanidinium groups, $^{13}$C containing quaternary amines and 180 containing betaines. Groups containing $^{2}$H or halogens like $^{37}$Cl or $^{8}$Br could also be employed. 

[0034] The present method is useful for quantitating rela› tive protein levels in complex protein mixtures and for determining the amino acid sequences of polypeptides. By using the phrase "determining the amino acid sequence", the present inventors do not intend to be limited to determining the entire sequence of a given polypeptide. Rather, by this phrase it is meant herein that a portion, portions, and/or the entire sequence is determined. 

[0035] The present methods involve addition of one or more relatively strong acid groups to the N-terminus of a polypeptide or one or more peptides thereof to produce one or more derivatized analytes for mass spectrometric analy› sis. The polypeptide/peptides are then analyzed using a mass spectrometric technique to provide a fragmentation pattern. The resulting fragmentation pattern is interpreted, thereby allowing sequencing of the polypeptide. 

## Methods of the Present Invention 

