Jun.29,2006  3  US 2006/0141632 Al  [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.  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.  [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  [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  Definitions  TABLE I  Three-letter  One-Letter  Average Amino Acid  Amino Acid  Abbreviation  Abbreviation  Residue Mass (Da)  Alanine  Ala  A  71.1  Arginine  Arg  R  156.2  Asparagine  Asn  N  114.1  Aspartic Acid  Asp  D  115.1  Cysteine  Cys  C  103.1  Glutamine  Gln  Q  128.1  Glutamic Acid  Glu  E  129.1  Glycine  Gly  G  57.1  Histidine  His  H  137.1  Isoleucine  Ile  113.2  Leucine  Leu  L  113.2  Lysine  Lys  K  128.2  Methionine  Met  M  131.2  Phenylalanine  Phe  F  147.2  Praline  Pro  p  97.1  Serine  Ser  s  87.1  Threonine  Thr  T  101.1  Tryptophan  Trp  w  186.2  Tyrosine  Tyr  y  163.2  Valine  Val  V  99.1 