Patent Publication Number: US-6905879-B2

Title: Isotope-coded ionization-enhancing reagents (ICIER) for high-throughput protein identification and quantitation using matrix-assisted laser desorption ionization mass spectrometry

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of the priority of U.S. Provisional Patent Application No. 60/242,645, filed Oct. 23, 2000. 
    
    
     BACKGROUND OF THE INVENTION 
     The present invention relates to the field of high-throughput protein analysis. More specifically, this invention relates to novel reagents for use in the identification and quantitation of proteins using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) in combination with peptide mass fingerprinting or fragment ion-based database searching. 
     MALDI-MS has become an established tool for the rapid identification of isolated proteins and has been used inter alia to identify proteins involved with human cancers, to elucidate components of multi-protein complexes, as well as for large-scale identification of proteins in organisms with fully sequenced genomes. Prior to MALDI-MS analysis, proteins/peptides are first separated by one-dimensional or two-dimensional polyacrylamide gel electrophoresis (1D or 2D-PAGE) or multidimensional liquid chromatography. Proteins/peptides are then identified by peptide mass mapping or fragment ion based database searching. Analytical procedures involving MALDI-MS are very robust, easy to automate, and most importantly, very fast both in terms of data acquisition and analysis. 
     However, peptide mass mapping may not routinely yield unambiguous protein identification with high confidence levels, particularly when only a few peptides are encountered. Furthermore, MALDI-MS often yields lower sequence coverage of proteins analyzed than electrospray ionization mass spectrometry (ESI-MS). This lower sequence coverage primarily results from both poor recovery of hydrophobic peptides during sample preparation and inefficient ionization of peptides without arginine residues by MALDI. In addition, MALDI-MS is intrinsically poor as a quantitation tool. Thus, it is very difficult to measure the relative abundance of proteins directly using MALDI-MS data. 
     There is a need in the art for additional reagents and methods for improving performance of MALDI-MS analysis of proteins/peptides both in terms of confident identification and accurate quantitation. 
     SUMMARY OF THE INVENTION 
     In one aspect, the invention provides a method for accurate relative quantitation of proteins using MALDI-MS. This method involves the following steps: reducing the disulfide bonds of proteins from a biological mixture; reacting the samples to be compared with a compound containing a guanidino group attached to a thiol reactive group via a linker which can be differentially labeled with either heavy or light isotopes (optionally prior to or following reduction); separating the proteins from the mixture; digesting the proteins; and subjecting them to quantitative mass spectrometric analysis. The compounds of the invention are also well suited for enhancing ionization efficiency of cysteine-containing peptides by MALDI-MS. This method is performed using the steps described above, with the following additional steps. The first sample is labeled with a reagent with isotopic substitutions and a second sample (e.g., a reference) is labeled with the equivalent reagent lacking these isotopic substitutions. Thereafter, the samples, or aliquots thereof, are mixed, prior to the separation step. After mixing, the modified proteins may be separated by 1D- or 2D-PAGE, gel bands or spots are cut and subjected to in-gel enzymatic digestion and subsequently MALDI-MS analysis. Alternatively, the mixed modified proteins may be subjected to enzymatic digestion and then the resulted peptides separated by various chromatographic steps before being subjected to MALDI-MS analysis. The proteins may be identified by peptide mass mapping or fragment-ion based data analysis and the relative protein abundance may be obtained by analyzing the relative peak intensity or peak area of the same peptide from two different samples. 
     In another aspect, the invention also provides a method for accurate relative quantitation and identification of proteins analyzed by electrospray MS. This method is performed in a manner similar to the method described above. 
     In yet another aspect, the invention provides novel reagents and reagent kits containing the compounds of the invention. 
     Other aspects and advantages of the present invention are described further in the following detailed description of the preferred embodiments thereof 
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     The inventors have identified a number of problems that cause the ambiguous results in both identification and relative quantitation of proteins using conventional approaches involving gel electrophoresis, MALDI-MS, and peptide mass mapping. More specifically, the inventors have found that the conventional 2D-PAGE/MALDI-MS/peptide mass mapping approach often provides inaccurate quantitation of proteins by gel image analysis and often ambiguous protein identifications. The inventors believe that poor ionization of certain peptides by MALDI is one of the main causes for ambiguous protein identifications. The present invention provides reagents and methods which overcome the defects in conventional MALDI-MS and peptide mass mapping methods. 
     Advantageously, the reagents of the invention can be used as cysteine-alkylating reagents, which provide many more peptide peaks in MALDI-MS than reagents previously described for use in MALDI-MS. This increase in peptide peaks observed when utilizing the reagents of the invention is due to the increased hydrophilicity and better ionization efficiency provided to the cysteine-containing peptides. Furthermore, because the methods of the invention utilize a mixture of light and heavy reagents, the exact number of cysteine residues in all peptide peaks observed by MALDI-MS can be determined. The resulting higher protein sequence coverage (more peptides observed) together with the knowledge of the exact number of cysteine residues in all peptides observed greatly increases the specificity of database searching using peptide mass fingerprinting. In fact, this additional information can make peptide mass fingerprinting routinely yield confident protein identifications and therefore makes the MALDI-MS combined with peptide mass fingerprinting a true high-throughput and yet unambiguous protein identification tool. The higher protein sequence coverage also permits a more complete chemical modification map of proteins to be obtained. Furthermore, the differential labeling strategy improves the currently popular 2D-PAGE-MS or 2D-LC-MS approaches in proteomics by increasing the dynamic range and accurately quantifying individual proteins. This improvement provides a much more complete picture of any proteome through the use of 2D-PAGE/2D-LC and MALDI-MS, thus increasing the possibility of finding protein drug targets that are differentially expressed in disease states. 
     Thus, the reagents of the invention are advantageous over conventional reagents for MALDI-MS analysis of proteins. These reagents can also be used for a variety of other purposes. These reagents and uses therefore are described in more detail below. 
     Compounds With Guanidino Functional Groups 
     Cysteine-containing peptides are often more hydrophobic due to the fact that disulfide bonds are usually buried inside of the globular proteins. Advantageously, the novel cysteine-modifying reagents of the invention not only increase the hydrophilicity of cysteine-containing peptides and thus minimize the loss of these hydrophobic peptides/proteins but also, more importantly, increase the ionization efficiency of these peptides by attachment of a guanidino functional group. Although not limited to such a use, these compounds are particularly well suited for use in MALDI-MS analysis. 
     In one embodiment, the compounds of the invention (ICIER) has a formula of A1-Linker-A2 which comprises a reactive group (A1) attached to an ionization enhancement group (A2) via a linker which can be differentially labeled with stable isotopes (Linker). Suitably, the ionization enhancement group is a strong basic functionality. In one embodiment, the ionization enhancement group (A2) is a guanidino group and has the formula: —NH—C(NH)—NH 2 . 
     The linker is any structure which may be differentially labeled with stable isotopes for use in quantitation and identification of proteins using MALDI-MS. In one embodiment, the linker contain from 1 to 100 atoms in length, about 3 to about 50 atoms in length, or about 5 to about 15 atoms in length, which are composed of carbon, and optionally, one or two atoms selected from O, S, NH, NR, NR′, CO, C(O)O, C(O)S, S—S, SO 2 , C(O)—NR′, CS—NR′, or Si—O. Optionally, one or more of the C atoms may be substituted with a small alkyl (C 1 -C 6 ), alkenyl, alkoxy, aryl, or diaryl groups. For example, the linker may be an alkyl, alkenyl, or alkynyl group, optionally substituted as described above. In another example, the linker may itself contain one or more O, S, NH, NR, NR′, CO, C(O)O, C(O)S, S—S, SO 2 , C(O)—NR′, CS—NR′, Si—O groups bound to one or more C atoms, which may be optionally substituted. In one embodiment, the linker is an alkyl group which contains a substitution of about four to about twelve atoms with a stable isotope. However, the linker may contain more than six isotope substitutions where desirable. For example, for peptides at the higher end of the molecular weight range at which MS is useful (e.g., about 2000 Da to 3500 Da) it may be desirable for the linker to contain eight, ten, twelve or more substitutions, in order to achieve the differential analysis required; whereas peptides at the lower end of the molecular weight range for MS (e.g., about 500 to 2000 Da) may require only four to six substitutions. For the selected number of substitutions, any one or more of the hydrogen, nitrogen, oxygen, carbon, or sulfur atoms in the linker may be replaced with their isotopically stable isotopes:  2 H,  13 C,  15 N,  17 O,  18 O, or  34 S. 
     The reactive group A1 reacts, preferably specifically, with thiols, and more particularly, with cysteine residues. Desirably, the thiol-reactive group is selected from the group consisting iodide, maleimide (see, for example, the structures below) 
                 
 
or α-haloacetyl groups such as X—CH 2 CO—. Most suitably, the X is selected from halogens such as iodine, bromine, and chorine to form iodoacetyl, bromoacetyl, or chloroacetyl functionalities.
 
     In another alternative, the thiol-reactive group may be selected from other α-, β-conjugated double bond structures, such as 
                 
 
and the like. Still other reactive groups can be readily synthesized to contain other thiol-specific reactive groups for use in binding cysteine-containing peptides.
 
     In certain preferred embodiments, a compound of the invention (ICIER) comprises a thiol-reactive group attached to a guanidino group by a linker, in which the formula of the compound is: 
                 
 
     While Compound C′ (one example of heavy ICIER) represents one particularly desirable isotopically heavy substituted version of Compound C (one example of Light ICIER), other isotopically heavy versions of this formula may be readily produced according to the present invention. Similarly, a variety of substitutions to Compounds A, B and D may be readily generated by one of skill in the art based on the teachings provided herein. 
     Synthesis of Reagents 
     The compounds of the invention may be readily synthesized by one of ordinary skill in the art utilizing the methods described in the examples below and techniques known to those of skill in the art. Some exemplary methods are illustrated in Example 1 below. 
     For example, a suitable starting material may be mixed with L-arginine in a mixture of tetrahydrofuran (THF) and water in a ratio of about 1 to about 1 parts by volume, for about 10 to about 48 hours, and most preferably about 16 hours at room temperature. The reaction mixture is then poured into acetone and the solid is collected. The solid is then dissolved in water and introduced into a suitable column, which is eluted with water to provide a compound of the invention. However, the invention is not so limited. For example, other suitable solvents may be substituted for the THF or acetone. Alternatively, the ratio of THF to water may be adjusted, as needed or desired. As another example, a salt of L-arginine (e.g., L-arginine D7-hydrochloride or L-argininamide dihydrochloride) may be dissolved in water and the pH adjusted to the basic range (e.g., about 8 to about 13, and more preferably about 8 to about 10), prior to reaction with iodoacetyl anhydride. Thereafter, the solid may be collected, e.g., by lowering the pH to the acid range (e.g., about 2 to about 4), filtering the resin and extracting the aqueous solution, followed by further filtration. The resulting solid may be freeze-dried to yield the desired compound. 
     However, given the descriptions provided herein, one of skill in the art will be able to readily select appropriate techniques and reagents for synthesis of compounds of the invention. 
     Following synthesis, the compounds are preferably purified to achieve the best results, particularly when they will be used in conjunction with 2D-PAGE, since reagents made in situ contain an excess of salt that will interfere with the first separation step of isoelectric focusing. Suitably, purification may be performed by filtration. Alternatively, other suitable methods may be readily selected by one of skill in the art. 
     These compounds may be utilized in a variety of methods in which protein/peptide labeling and/or increasing the ionization of cysteine-containing peptides is desired. However, the compounds are particularly useful in methods for high-throughput protein identification and quantitation using MALDI-MS. 
     Methods of Using the Compounds of the Invention 
     The compounds of the invention are particularly useful in methods for quantitation and identification of one or more proteins in a mixture. Suitably, the peptides analyzed by the method of the invention are between about 500 Daltons (Da) to about 3500 Daltons. The protein mixture may be a sample from a cell or tissue culture, or biological fluids, cells or tissues. Samples from a culture include cell homogenates and cell fractions. Biological fluids include urine, blood (including, e.g., whole blood, plasma and sera), cerebrospinal fluid, tears, feces, saliva, and lavage fluids. The mixtures may include proteins, lipids, carbohydrates, and nucleic acids. The methods of the invention employ MS and (MS) n  methods. Currently, matrix assisted laser desorption ionization MS (MALDI/MS) and electrospray ionization MS (ESI/MS) methods are preferred. However, a variety of other MS and (MS) n  techniques may be selected. 
     In one embodiment, the invention provides a method for quantitative analysis of a proteome (i.e., a complex mixture containing proteins and/or peptides) using the compound of the invention. Typically, a sample is obtained from a source, as defined above. Where isolated proteins will be identified using techniques based on MALDI-MS and peptide mass mapping, the sample may be compared to a reference protein mixture, which is obtained as a sample from the same source or may be obtained from another source. Alternatively, isolated proteins may be identified using post-source delay (PSD) or collision-induced dissociation (CID) techniques followed by fragment ion-based database searching (M. Mann and M. Wilm,  Anal. Chem.,  66: 4390 (1994)) or de novo sequencing, and the sample may be compared to a reference protein mixture using MS data. The sample protein mixture and the reference protein mixture are processed separately, applying identical reaction conditions, with the exception that only one mixture (e.g., the sample) will be reacted with the compound containing isotopically stable isotopes. Alternatively, where relative quantitation of proteins is not desirable, no reference samples are required; nor are isotopically heavy equivalents of the compounds of the invention required. Optionally, any labeling reaction step may be performed prior to, or following, the other method steps which are described herein. 
     Typically, the protein sample is dissolved in a buffer suitable for 1D-PAGE or 2D-PAGE or in-solution enzymatic digestion. Such buffers may be purchased commercially from a variety of sources (e.g., Genomic Solutions, Ann Arbor, Mich.; BioRad, Hercules, Calif.) or prepared according to known methods. Throughout the following method steps, the pH of the mixture is maintained under neutral or basic conditions. Most suitably, the pH is maintained between 7 and 10. Preferably, the method of the invention is performed at a basic pH where the compound of the invention containing the guanidino group (e.g., compounds A, B, C, C′ and D) is utilized. Most suitably, the pH is in the range of about 8 to about 9, and most preferably about 8.5. Alternatively, the method of the invention is preferably performed at a neutral pH where a compound of the invention containing a maleimide affinity tag is utilized. In this circumstance, the method is preferably performed at a pH of about 6.5 to about 8.5, more preferably 7 to 8, and most preferably 7 to 7.5. 
     Following preparation of the sample and reference, the disulfide bonds of the proteins in the sample(s) or reference mixtures are reduced to free SH groups. Suitable reducing agents include tri-n-butylphosphine, mercaptoethylamine, dithiothreitol (DTT), and tricarboxyethylphosphine, which are used in excess. However, other suitable reducing agents may be substituted. In one embodiment, disulfide bonds are denatured using 50 mM Tris buffer, 6M guanidine HCl, 5 mM tributyl phosphine at pH 8.5 for 1 hour at 37° C. However, other reducing agents, buffered to a pH in the basic range may be selected and incubated for varying lengths of times at room temperature. 
     Where no protein quantitation is to be performed, no reference sample need be labeled, and the following parallel reaction steps with equivalent heavy or light ICIER and mixing steps can be eliminated. Where protein quantitation will be performed, a selected compound of the invention, either an isotopically heavy or light compound, will be reacted with the samples to be compared. This labeling reaction step may be performed prior to, or following, the other method steps which are described herein. Typically, the reference sample is labeled with the isotopically heavy compound and the experimental sample(s) are labeled with the isotopically light form of the compound. However, the labeling may be reversed. Following reduction and reaction with the selected labeling reagents (heavy or light ICIER), defined aliquots of the samples (optionally labeled with isotopically different compounds, e.g., corresponding light and heavy compounds) are combined and all the subsequent steps are performed on the pooled samples. Preferably, equal amounts of the samples are combined. 
     Suitably, prepared gels for one-dimensional (1D) or two-dimensional (2D) polyacrylamide gel electrophoresis (PAGE) may be obtained from a variety of commercial sources and used according to manufacturer&#39;s instruction (Genomics Solutions; Ann Arbor, Mich.; NOVEX, San Diego, Calif.). However, the invention is not so limited. One of skill in the art can readily apply other techniques for separating the ICIER-labeled proteins. 
     Following mixing of the ICIER-treated samples, the proteins are separated by 1D-PAGE or 2D-PAGE. Then the protein bands or spots of interest are cut and subjected to enzymatic digestion. Suitably, the proteins may be subjected to in-gel digestion using techniques which have been described previously (e.g., Rosenfeld et al,  Anal. Biochem.,  203:173-179 (1992) and Sechi et al,  Anal. Chem.,  70:5150-5158 (1998)), or the modification thereof as described in the examples below. 
     A suitable protease for use in this enzymatic digestion method may be readily selected from among proteases which are compatible with the basic conditions and the procedure. In one embodiment, the protease is trypsin. In another embodiment, a mixture of proteases which have similar activity levels at basic pH is used. Such proteases may include aminopeptidases, carboxypeptides, among others. Alternatively, protein digestion may be omitted where the proteins to be analyzed are small (e.g., about 500 to 1000 Da). 
     Suitably, the peptides are extracted from the gel using conventional techniques. For example, following destaining, the peptides may be extracted by adding a solution of acetonitrile and trifluoroacetic acid (TFA) to the gel band and incubating, before collecting the liquid phase. This step may be repeated and additional acetonitrile added to complete the extraction. The extract solutions are pooled and dried, then reconstituted with a solution of acetonitrile and TFA. Other suitable methods for peptide extraction are well known to those of skill in the art and may be readily utilized. 
     The isolated, derivatized peptides are then analyzed using MS techniques. Both the relative quantity and sequence identity of the proteins from which the labeled peptides originated can be determined by MALDI-MS techniques (i.e. MS and MS n (PSD, CID)) and subsequent data analysis (i.e. peptide mass mapping or fragment-ion based data analysis). Preferably, the relative quantitation of proteins is obtained from MS data, while the protein identification can derived from the analysis of either MS data (peptide mass mapping) or MS n  data (fragment ion based database searching). 
     Apparatuses for performing MALDI-MS, and techniques for their use, are described in International Publication WO 93/24835, U.S. Pat. No. 5,288,644, R. Beavis and B. Chait,  Proc. Natl. Acad. Sci. USA,  87:6873-6877 (1990); B. Chait and K. Standing, Int.  J. Mass Spectrom, Ion Phys.,  40:185 (1981) and Mamyrin et al,  Sov. Phys. JETP,  37:45 (1973), all of which are incorporated by reference herein. Briefly, the frequency tripled output of, e.g., a Q-switched Lumonics HY400 neodymium/yttrium aluminum garnet lawer (“Nd-YAG”) (355 nm, 10-nsec output pulse) is focused by a lens (12-inch focal length) through a fused silica window onto a sample inside the mass spectrometer. The product ions formed by the laser are accelerated by a static electric potential of 30 kV. The ions then drift down a 2-m tube maintained at a vacuum of 30 μPa and their arrival at the end of the tube is detected and recorded using, e.g., a Lecroy TR8828D transient recorder. The transient records of up to 200 individual laser shots are summed together and the resulting histogram is plotted as a mass spectrum. Peak centroid determinations and data reduction can be performed using a VAX workstation or other computer system. 
     However, other MS techniques, including electrospray ionization (ESI)/MS, among others, may be readily utilized to analyze the proteins and peptides modified by the compounds of the invention (ICIER). 
     Reagent Kit 
     The invention further provides a reagent kit for the analysis of proteins by mass spectral analysis. Typically, such a kit will contain one or more compounds of the invention. Most suitably, the kit will contain a set of substantially identical, differentially labeled (isotopically light and heavy) compounds. The kit may further contain one or more proteolytic enzymes, reaction buffers, or wash solutions. 
     The method and kit of the invention may be used for a variety of clinical and diagnostic assays, in which the presence, absence, deficiency or excess of a protein is associated with a normal or disease state. The method and kit of the invention can be used for qualitative and quantitative analysis of protein expression in cells and tissues. The method and kit can also be used to screen for proteins whose expression levels in cells or biological fluids is affected by a drug, toxin, environmental change, or by a change in condition or cell state, e.g., disease state, malignancy, site-directed mutation, gene therapy, or gene knockouts. 
     The following examples are provided to illustrate the invention and do not limit the scope thereof. One skilled in the art will appreciate that although specific reagents and conditions are outlined in the following examples, modifications can be made which are meant to be encompassed by the spirit and scope of the invention. 
     EXAMPLE 1 
     Reagents of the Invention 
     This example illustrates methods for synthesis of exemplary compounds A, B, C, C′ and D of the invention. These compounds are useful as reagents in MALDI-MS and peptide mass mapping, as shown in the following examples. 
     1. 2-(2-(2,5-dioxo-2,5-dihydro-pyrrol-1-yl)-acetylamino)-5-guanidino-pentanoic Acid or Maleimidoacetyl Arginine (A):
         (2,5-Dioxo-2,5-dihydro-pyrrol-1-yl)-acetic acid-2,5-dioxo-pyrrolidin-1-yl ester (4.8 g, 19 mmol) and L-arginine (2.9, 17 mmol) was stirred in 30 mL of a mixture of tetrahydrofuran (THF) and water, THF:H 2 O (1:1), for 16 hours at room temperature. The reaction mixture was poured into acetone (1.5 L) and the solid was collected. The solid was dissolved in H 2 O (3 mL) and then introduced onto Bakerbond (Octadecyl (C18) 40 μm prep LC Packing) column, and eluted with water to give 1.1 g of product.  1 H NMR (D 2 O, 300 MHZ): 6.8 (s, 2H), 4.3 (H a , d, J=16.9 Hz, 1H), 4.2 (H b , d, J=16.9 Hz, 1H), 4.1 (dd, J=4.9, 7.7 Hz, 1H), 3.1 (t, J=6.9 Hz, 2H), 1.8-1.5 (m, 4H).       

     2. 2-(3-2,5-dioxo-2,5-dihydro-pyrrol-1-yl)-propionylamino)-5-guanidino-pentanoic Acid or Maleimidopropionyl Arginine (B):
         3-(2,5-dioxo-2,5-dihydro-pyrrol-1-yl)-propionic acid-2,5-dioxo-pyrrolidin-1-yl ester (7.6 g, 28.5 mmol) and L-arginine (4.3 g, 25 mmol) was stirred in 50 mL of a mixture of THF:H 2 O (1:1) for 16 hr at room temperature. The reaction mixture was poured into acetone (1.5 L) and the solid was collected. The solid was dissolved in H 2 O (5 mL) and then introduced onto Bakerbond (Octadecyl (C18) 40 μm prep LC Packing) column, and eluted with water to give 1.5 g of product.  1 H NMR (D 2 O, 300 MHZ): 6.8 (s, 2H), 4.1 (dd, J=4.7, 7.4 Hz, 1H), 3.8 (m, 2H), 3.2 (t, J=6.9 Hz, 2H), 2.5 (m, 2H), 1.7-1.5 (m, 4H).       

     3. N-α-(Iodoacetyl)-L-arginine (C):
         L-Arginine (8.0 g, 45.6 mmol) was dissolved in deionized water (75 mL) and was reacted with iodoacetic anhydride (21.0 g, 59.3 mmol) with vigorous stirring for 15 min while the pH was maintained between 8 and 9.5 with Dowex 1x2-100 (OH − ). The pH was allowed to drop to ˜4 (5-10 min) and 55% aqueous hydriodic acid was added to bring the pH to 2. The resin was filtered and the aqueous hydriodic acid was extracted with diethyl ether (3×250 ml). The aqueous layer was neutralized with Dowex 1x2-100 (OH − ) to pH 8-9, the resin was filtered and washed with water and the resulting solution was freeze-dried to afford N-α-(Iodoacetyl)-L-arginine (11.9 g, 76% overall yield) as a fluffy white powder.  1 H NMR (D 2 O) δ 1.52-1.88 (m, 4H), 3.12 (t, 2H, J=6.7 Hz), 3.76 (d, 1H, J=10.2 Hz), 3.76 (d, 1H, J=10.4 Hz), 4.06-4.10 (m, 1H);  13 C NMR (D 2 O) δ-2.0, 24.5, 28.8, 40.7, 55.1, 156.8, 171.5, 178.3. Molecular formula: C 18 N 15 N 4 IO 3 .       

     4. N-α-(Iodoacetyl)-L-arginine-D 7  (C′):
         L-arginine-D 7  hydrochloride (5.2 g, 28.73 mmol) was dissolved in deionized water (50 mL) and the pH was adjusted to 8 with Dowex 1x2-100 (OH − ). It was then reacted with iodoacetic anhydride (15.5 g, 43.78 mmol) as above to afford N-α-(Iodoacetyl)-L-arginine-D 7  (5.5 g, overall yield 55%/o) as a fluffy white powder.  1 H NMR (D 2 O) δ 3.74 (d, 1H, J=10.2 Hz), 3.82 (d, J=10.4 Hz). Molecular formula: C 8 H 8 D 7 N 4 IO 3 .       

     5. N-α-(Iodoacetyl)-L-argininamide hydrochloride (D):
         L-Argininamide dihydrochloride (10.5 g, 42.6 mmol) was dissolved in deionized water (75 mL) and the pH was adjusted to 13 with Dowex 1x2-100 (OH − ). Then it was reacted with iodoacetic anhydride (18.0 g, 50.85 mmol) with vigorous stirring for 15 min while the pH was maintained between 8 and 9.5 with Dowex 1x2-100 (OH − ). The pH was allowed to drop to ˜4 (5-10 min) and 55% aqueous hydriodic acid was added to bring the pH to 2. The resin was filtered and the aqueous solution was extracted by diethyl ether (3×250 ml). The aqueous layer was filtered through a pad Dowex Retardion 11A8 (50 g) and washed with water. The resultant solution was freeze-dried to afford N-α-(Iodoacetyl)-L-argininamide hydrochloride (11.1 g, 69%) as a fluffy white powder.  1 H NMR (D 2 O) δ 1.62-2.02 (m, 4H), 3.24 (t, 2H, J=6.6 Hz), 3.79 (d, 1H, J=10.2 Hz), 3.89 (d, 1H, J=10.7 Hz), 4.27-4.31 (m, 1H);  13 C NMR (D 2 O) δ-2.7, 24.5, 28.3, 40.6, 53.6, 156.9, 172.5, 176.3. Molecular formula: C 8 H 16 N 5 IO 2 .HCl.       

     EXAMPLE 2 
     Comparative Example Demonstrating Ionization Enhancement-MALDI-MS Analysis of Six Separate Model Proteins after Treatment with Either the Reagent of the Invention (Light Icier) or a Conventional Reagent (IAA) 
     A. Reduction:
         90 μg each of the six model proteins, CTLA-4-IgGl, Interleukin-12 (IL-12), α-Lactalbumin, Trypsinogen, Lysozyme, and Ribonuclease, were dissolved separately in 30 μL of the reaction buffer containing 5% SDS, 20% glycerol, and 750 mM Tris-HCl (pH 8.45) to obtain solutions of 3 μg/μL. To each solution was added a 200-fold excess (with regard to cysteine content per protein) of dithiothreitol (DTT). The reduction was allowed to proceed for 30 minutes at 90° C., followed by cooling of the solutions for 10 minutes.       

     B. Cysteine Modification:
         Reagent C (light ICIER) was synthesized as described in Example 1. Each of the six proteins was alkylated using both reagent C and iodoacetamide separately. The amount of the alkylating reagent (reagent C or iodoacetamide) was equivalent to a five-fold excess with regard to the amount of DTT used in step A. The alkylations were allowed to proceed for 1 hour at room temperature. Then 0.1 μg of each protein labeled by reagent C was mixed with 0.1 μg of the same protein but alkylated by iodoacetamide. Each of the six resultant protein solutions was then mixed in a 1:1 ratio (volume to volume) with 2× Tricine loading buffer.       

     C. Gel Electrophoresis and Staining:
         Each of the final resultant protein solutions described in Part B (each solution contains 0.2 μg of one of the six proteins) was loaded onto a 10%, 10-well Tricine mini-gel (Novex, San Diego, Calif.). The gels were run according to the manufacturer&#39;s instructions and stained with Coomassie Blue G-250.       

     D. In-Gel Digestion:
         Automated in-gel digestion of proteins was carried out using a 96-well ProGest (Genomic Solutions, Ann Arbor, Mich.) with a procedure modified from Rosenfeld et al,  Anal. Biochem.,  203:173-179 (1992) and Sechi et al,  Anal. Chem.,  70:5150-5158 (1998). Briefly, gel bands were cut into 1×1 mm pieces and then destained by washing sequentially with 50 μL each of the following solutions: (1) 200 mM NH 4 HCO 3 , (2) 50% methanol/10% acetic acid; (3) 40% ethanol/water and incubated for 10 minutes for each step. The three washing steps were repeated 5 times and then 100 μL of 10 nM NH 4 HCO 3  was added and incubated for 10 minutes. The gel pieces were then dehydrated by addition of 2×100 μL of acetonitrile. After removing the excess acetonitrile, the gels were rehydrated with 25 μL of a solution containing 625 ng of trypsin in 10 mM NH 4 HCO 3  and incubated at 37° C. for 10 hours. Peptides were extracted by adding 30 μL of a solution of 50% acetonitrile/0.5% trifluoroacetic acid (TFA) and incubated for 10 minutes before collecting the liquid phase. This step was repeated one more time and then 30 μL of acetonitrile was added to complete the extraction. The extracted solutions were pooled together and dried completely with a SpeedVac (Savant, Holbrook, N.Y.). Finally, the dried peptide samples were reconstituted with 20 μL of an acetonitrile/water/TFA (50:50:1) solution.       

     E. MALDI Mass Spectrometry
         Molecular weights of all peptides were determined by analyzing one-twentieth of the reconstituted peptide solution employing a matrix-assisted laser desorption ionization (MALDI) delayed extraction (DE) reflectron time-of-flight (TOF) instrument (Voyager DE-STR, PE Biosystems, Framingham, Mass.) equipped with a nitrogen laser (337 nm) in reflectron mode. Peptides were crystallized by mixing 0.8 μL of the sample solution with 0.8 PL of a matrix solution containing saturated α-cyano-4-hydroxycinnamic acid in 0.5% TFA/50% acetonitrile/water. Spectra were externally calibrated using a mixture of known peptides.   Peak tables were generated from each spectrum and the data were used to create the ionization enhancement and peak ratio tables presented herein.   The following tables summarize the results of the MALDI-MS analysis of the six protein samples after treatment with reagent C (ICIER) or iodoacetamide (IAA) and the comparison of the same. See Tables I-XVIII.       

     
       
         
           
               
             
               
                 TABLE I 
               
             
            
               
                   
               
               
                 CTLA4-alkylated with IAA 1:1 (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
               
                 1161.6112 
                 1161.6302 
                 1991 
               
               
                 N/A 
                 1171.5491 
                 N/A 
               
               
                 1187.5239 
                 1187.5441 
                 1452 
               
               
                 1485.7119 
                 1485.7048 
                 7944 
               
               
                 2138.9793 
                 2139.028  
                 7551 
               
               
                 2801.3180 
                 2801.2677 
                 1253 
               
               
                  2817.9851* 
                 2817.2626 
                 1567 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 11  
               
               
                 Number of Cysteines Detected: 5  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE II 
               
             
            
               
                   
               
               
                 CTLA4-IgG alkylated with Reagent C (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
            
           
           
               
               
               
            
               
                 1318.7222 
                 1318.7153 
                 10610 
               
               
                 1328.6746 
                 1328.6343 
                 3035 
               
               
                 1344.6331 
                 1344.6292 
                 3922 
               
               
                 1642.7809 
                 1642.7899 
                 22134 
               
               
                 2296.0863 
                 2296.1131 
                 8587 
               
               
                 2958.3574 
                 2958.3528 
                 1442 
               
               
                 2974.3377 
                 2974.3477 
                 1210 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 11  
               
               
                 Number of Cysteines Detected: 5  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE III 
               
             
            
               
                   
               
               
                 Comparison of Data for CTLA4-IgG 
               
            
           
           
               
               
               
            
               
                 Height Ratio for 
                   
                   
               
               
                 CTLA4-IgG (Reagent C/IAA) 
                 Peptide Sequence 
                 SEQ ID NO: 
               
               
                   
               
               
                 5.33 
                 (K)NQVSLTCLVK(G) 
                 1 
               
               
                 N/A 
                 (R)AMDTGLYICK(V) 
                 2 
               
               
                 2.70 
                 (R)AMDTGLYICK(V) 
                 2 
               
               
                 2.79 
                 (R)GIASFVCEYASPGK(A) 
                 3 
               
               
                 1.14 
                 (R)TPEVTCVVVDVSHEDPVK(F) 
                 4 
               
               
                 1.15 
                 (R)WQQGNVFSCSVMHEALHNHYTQL(S) 
                 5 
               
               
                 0.77 
                 (R)WQQGNVFSCSVMHEALHNHYTQK(S) 
                 5 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE IV 
               
             
            
               
                   
               
               
                 IL-12 alkylated with IAA (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
            
           
           
               
               
               
            
               
                 N/A 
                 907.4671 
                 N/A 
               
               
                 1412.5917 
                 1412.5905 
                 6566 
               
               
                 N/A 
                 1795.7274 
                 N/A 
               
               
                 1863.8916 
                 1863.8507 
                 6089 
               
               
                 2206.1381 
                 2206.0895 
                  782 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 9  
               
               
                 Number of Cysteines Detected: 3  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE V 
               
             
            
               
                   
               
               
                 IL-12 alkylated with Reagent C (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
               
                 1064.5402 
                 1064.5523 
                 2411 
               
               
                 1569.7046 
                 1569.6756 
                 9028 
               
               
                 1952.8747 
                 1952.8125 
                 5441 
               
               
                 2020.9710 
                 2020.9358 
                 4543 
               
               
                 2363.2748 
                 2363.1746 
                 1181 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 9  
               
               
                 Number of Cysteines Detected: 5  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE VI 
               
             
            
               
                   
               
               
                 Comparison of Data for IL-12 
               
            
           
           
               
               
               
            
               
                 Height Ratio for IL-12 
                   
                   
               
               
                 (Reagent C/IAA) 
                 Peptide Sequence 
                 SEQ ID NO: 
               
               
                   
               
            
           
           
               
               
               
            
               
                 N/A 
                 (K)TSATVICR(K) 
                 6 
               
               
                 1.37 
                 (K)EFGDAGQYTCHK(G) 
                 7 
               
               
                 N/A 
                 (R)YYSSSWSEWASVPCS(−) 
                 8 
               
               
                 0.75 
                 (R)GSSDPQGVTCGAATLSAER(V) 
                 9 
               
               
                 1.51 
                 (R)FTCWWLTTISTDLTFSVK(S) 
                 10 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE VII 
               
             
            
               
                   
               
               
                 α-Lactoalbumin alkylated with IAA (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
               
                 none 
                  707.3398 
                 N/A 
               
               
                 1091.51432 
                 1091.5196 
                 6131 
               
               
                 none 
                 1715.7508 
                 N/A 
               
               
                 1779.83739 
                 1779.8410 
                 3436 
               
               
                 none 
                 1843.8458 
                 N/A 
               
               
                 1892.92914 
                 1892.9250 
                 7606 
               
               
                 2003.914  
                 2003.8187 
                 overlap 
               
               
                 2591.27206 
                 2591.1077 
                 3115 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 8  
               
               
                 Number of Cysteines Detected: 5  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE VIII 
               
             
            
               
                   
               
               
                 α-Lactoalbumin alkylated with Reagent C (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
            
           
           
               
               
               
            
               
                  864.42181 
                  864.4249 
                 6976 
               
               
                 1248.60859 
                 1248.6047 
                 33460 
               
               
                 1872.83547 
                 1872.8359 
                 17483 
               
               
                 2093.96824 
                 2094.0112 
                 3307 
               
               
                 2000.93299 
                 2000.9309 
                 11339 
               
               
                 2207.10324 
                 2207.0953 
                 7629 
               
               
                 2317.96953 
                 2317.989  
                 5207 
               
               
                 none 
                 3062.3631 
                 N/A 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 8  
               
               
                 Number of Cysteines Detected: 7  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE IX 
               
             
            
               
                   
               
               
                 Comparison of Data for α-Lactoalbumin 
               
            
           
           
               
               
               
            
               
                 Height Ratio for 
                   
                   
               
               
                 α-Lactoalbumin 
               
               
                 (Reagent C/IAA) 
                 Peptide Sequence 
                 SEQ ID NO: 
               
               
                   
               
               
                 N/A 
                 (K)ALCSEK(L) 
                 aa 1-8 of SID NO:11 
               
               
                 5.46 
                 (K)LDQWLCEK(L) 
                 aa 7-16 of SID NO:11 
               
               
                 N/A 
                 (K)FLDDDLTDDIMCVK(K) 
                 aa 1-16 of SID NO:12 
               
               
                 0.96 
                 (K)ALCSEKLDQWLCEK(L) 
                 11 
               
               
                 N/A 
                 (K)FLDDDLTDDIMCVKK(I) 
                 12 
               
               
                 1.00 
                 (K)ALCSEKLDQWLCEKL(−) 
                 11 
               
               
                 N/A 
                 (K)DDQNPHSSNICNISCDK(F) 
                 aa 5-23 of SID NO:12 
               
               
                 N/A 
                 (K)IWCKDDQNPHSSNICNISCDK(F) 
                 13 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE X 
               
             
            
               
                   
               
               
                 Lysozyme alkylated with IAA (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
            
           
           
               
               
               
            
               
                 N/A 
                 505.2557 
                 N/A 
               
               
                 none 
                 577.2880 
                 N/A 
               
               
                  993.4044 
                 993.4001 
                 16094 
               
               
                 1065.4958 
                 1065.5185 
                 5466 
               
               
                 1325.6148 
                 1325.6312 
                 7685 
               
               
                 1333.6643 
                 1333.6687 
                 25788 
               
               
                 N/A 
                 1491.6552 
                 Buried 
               
               
                 2181.0465 
                 2181.0300 
                 8876 
               
               
                 2508.5231 
                 2508.29788 
                 2902 
               
               
                 2735.4461 
                 2735.2636 
                 2672 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 9  
               
               
                 Number of Cysteines Detected: 5  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE XI 
               
             
            
               
                   
               
               
                 Lysozyme alkylated with Reagent C (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
            
           
           
               
               
               
            
               
                 662.3187 
                 662.3408 
                 11061 
               
               
                 734.3755 
                 734.3732 
                 2407 
               
               
                 1150.4807 
                 1150.4852 
                 9782 
               
               
                 1222.5917 
                 1222.6036 
                 9199 
               
               
                 1428.6595 
                 1428.7164 
                 56959 
               
               
                 1490.7545 
                 1490.7538 
                 24700 
               
               
                 1648.7478 
                 1648.7403 
                 8750 
               
               
                 2338.1091 
                 2338.1151 
                 5656 
               
               
                 2979.3921 
                 2979.4450 
                 1867 
               
               
                 2892.4820 
                 2892.3487 
                 2113 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 9  
               
               
                 Number of Cysteines Detected: 8  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE XII 
               
             
            
               
                   
               
               
                 Comparison of Data for Lysozyme 
               
            
           
           
               
               
               
            
               
                 Height Ratio for Lysozyme 
                   
                   
               
               
                 (Reagent C/IAA) 
                 Peptide Sequence 
                 SEQ ID NO: 
               
               
                   
               
               
                 N/A 
                 (R)GCRL(−) 
                 14 
               
               
                 N/A 
                 (R)NRCK(G) 
                 15 
               
               
                 0.61 
                 (R)WWCNDGR(T) 
                 aa 1-9 of SID NO:18 
               
               
                 1.68 
                 (R)CELAAAMKR(H) 
                 16 
               
               
                 7.41 
                 (R)GYSLGNWVCAAK(F) 
                 aa 1-14 of SID NO:21 
               
               
                 0.96 
                 (R)CKGTDVQAWIR(G) 
                 17 
               
               
                 N/A 
                 (R)WWCNDGRTPGSR(N) 
                 18 
               
               
                 0.64 
                 (R)HGLDNYRGYSLGNWVCAAK(F) 
                 19 
               
               
                 0.64 
                 (R)NLCNIPCSALLSSDITASVNCAK(K) 
                 20 
               
               
                 0.79 
                 (R)GYSLGNWVCAAKFESNFNTQATNR(N) 
                 21 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE XIII 
               
             
            
               
                   
               
               
                 Ribonuclease A alkylated with IAA (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
            
           
           
               
               
               
            
               
                 1504.6742 
                 1504.6825 
                 6041 
               
               
                 2224.0861 
                 2224.1065 
                 22526 
               
               
                 2517.2230 
                 2517.2890 
                 14079 
               
               
                 2867.4150 
                 2867.5666 
                 4222 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 8  
               
               
                 Number of Cysteines Detected: 4  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE XIV 
               
             
            
               
                   
               
               
                 Ribonuclease A alkylated with Reagent C (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
            
               
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
               
            
           
           
               
               
               
            
               
                 1661.7593 
                 1661.7785 
                 16953 
               
               
                 2381.1712 
                 2381.1743 
                 46801 
               
               
                 2831.3933 
                 2831.3889 
                 9332 
               
               
                 3024.5002 
                 3024.7205 
                 4879 
               
               
                   
               
               
                 Theoretical Number of Cysteines: 8  
               
               
                 Number of Cysteines Detected: 5  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE XV 
               
             
            
               
                   
               
               
                 Comparison of Data for Ribonuclease 
               
            
           
           
               
               
               
            
               
                 Height Ratio for Ribonuclease 
                   
                   
               
               
                 (Reagent C/IAA) 
                 Peptide Sequence 
                 SEQ ID NO: 
               
               
                   
               
               
                 2.81 
                 (R)ETGSSKYPNCAYK(T) 
                 22 
               
               
                 2.08 
                 (K)HIIVACEGNPYVPVHFDASV(−) 
                 aa 7-27 of SID No.24 
               
               
                 0.66 
                 (R)CKPVNTFVHESLADVQAVCSQK(N) 
                 23 
               
               
                 1.16 
                 (K)TTQANKHIIVACEGNPYVPVHFDASV(−) 
                 24 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE XVI 
               
             
            
               
                   
               
               
                 Trypsinogen alkylated with IAA (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
               
            
               
                   
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
                   
               
               
                   
                 1168.59697 
                 1168.5825 
                 5577 
               
               
                   
                 none 
                 1077.5250 
                 N/A 
               
               
                   
                 none 
                 1478.7347 
                 N/A 
               
               
                   
                 1490.75058 
                 1490.7426 
                 4891 
               
               
                   
                 1609.68206 
                 1609.6586 
                 1573 
               
               
                   
                 none 
                 2267.0110 
                 N/A 
               
               
                   
                   
               
               
                   
                 Theoretical Number of Cysteines: 12  
               
               
                   
                 Number of Cysteines Detected: 3  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE XVII 
               
             
            
               
                   
               
               
                 Trypsinogen alkylated with Reagent C (1:1 @ 0.1 g/band) 
               
            
           
           
               
               
               
               
            
               
                   
                 Detected Mass (Da) 
                 Theoretical Mass (Da) 
                 Height 
               
               
                   
                   
               
            
           
           
               
               
               
               
            
               
                   
                 1325.68371 
                 1325.6676 
                 24135 
               
               
                   
                 1234.6102 
                 1234.61265 
                 12845 
               
               
                   
                 1792.94896 
                 1792.9050 
                 2455 
               
               
                   
                 1647.85269 
                 1647.8277 
                 14787 
               
               
                   
                 1923.88166 
                 1923.8289 
                 2795 
               
               
                   
                 2424.06382 
                 2424.0964 
                 3046 
               
               
                   
                   
               
               
                   
                 Theoretical Number of Cysteines: 12  
               
               
                   
                 Number of Cysteines Detected: 7  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE XVIII 
               
             
            
               
                   
               
               
                 Comparison of Data for Trypsinogen 
               
            
           
           
               
               
               
            
               
                 Height Ratio for Trypsinogen 
                   
                   
               
               
                 (Reagent C/IAA) 
                 Peptide Sequence 
                 SEQ ID NO: 
               
               
                   
               
               
                 4.33 
                 (K)VCNYVSWIK(Q) 
                 25 
               
               
                 N/A 
                 (K)APILSDSSCK(S) 
                 26 
               
               
                 N/A 
                 (K)CLKAPILSDSSCK(S) 
                 27 
               
               
                 3.02 
                 (K)LQGIVSWGSGCAQK(N) 
                 28 
               
               
                 1.78 
                 (K)DSCQGDSGGPVVCSGK(L) 
                 29 
               
               
                 N/A 
                 (K)SAYPGQITSNMFCAGYLEGGK(D) 
                 30 
               
               
                   
               
            
           
         
       
     
     From these data, it was concluded that, compared to the conventional cysteine-alkylating reagent Iodoacetamide, ICIER greatly increases the ionization efficiency of cysteine-containing tryptic peptides with a lysine residue at their C-terminus. For example, in the MALDI-MS spectrum of tryptic peptides from lysozyme modified by both reagent C and IAA (see Table XII), the intensity of a peptide modified by reagent C (GYSLGNWVCAAK, aa 2-13 of SEQ ID NO:21, molecular weight, 1428.72 Da) is 7.4 times that of the same peptide modified by IAA (molecular weight, 1325.63 Da). Moreover, mass peaks for many cysteine-containing peptides with a lysine residue at their C-terminus that were absent when using IAA became well observed when using ICIER. On the other hand, ICIER modification did not have any significant effect on the ionization of peptides with an arginine residue at their C-terminus. As a result, the overall number of cysteine-containing peptides detected by MALDI-MS is also increased, and hence the sequence coverage obtained for proteins being analyzed when using ICIER is much higher than that when using iodoacetamide. 
     EXAMPLE 3 
     Protein Quantitation by Icier and MALDI-MS Using CTLA4-IgG as a Model Protein 
     Different amounts of CTLA4-IgG with ratios of 1:1, 1:1.5, 1:2, 1:5, and 1:10 were reduced by DTT as described in EXAMPLE 2. The samples to be compared were alkylated with either light or heavy ICIER and then mixed together before being subjected to gel electrophoresis, protein staining, in-gel digestion, and MALDI-MS analysis using the same conditions described in EXAMPLE 2. 
     Table XIX summarizes the labeling of CTLA4-IgG at different ratios using light and heavy ICIER. Peptide masses were all externally calibrated using default calibration files. The relative quantitation of the protein from two different pools was determined by averaging the mass intensity ratios between all seven pairs of peptides labeled by light and heavy ICIER. 
     
       
         
           
               
               
               
               
             
               
                 TABLE XIX 
               
               
                   
               
               
                 Theor. 
                   
                   
                   
               
               
                 Mass (Da) 
                 Peptide Sequence 
                 SEQ ID NO: 
                 Observed Ratios* 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 1318.72 
                 (K)NQVSLTCLVK(G) 
                 1 
                 
                   1.23 
                 
                 
                   1.64 
                 
                 
                   2.29 
                 
                   4.22   
                   8.9   
               
               
                 1328.63 
                 (R)AMDTGLYICK(V) 
                 2 
                 
                   0.88 
                 
                 
                   0.62 
                 
                 
                   1.43 
                 
                   0.61   
                   0.7   
               
               
                 1374.63 
                 (R)AMDTGLYICK(V) 
                 2 
                 0.95 
                 1.39 
                 2.01 
                  4.31 
                  8.2 
               
               
                 1642.79 
                 (R)GIASFVCEYASPGK(A) 
                 3 
                 0.96 
                 1.39 
                 1.86 
                  3.68 
                 10 
               
               
                 2296.11 
                 
                   (R)TPEVTCVVVDVSHEDPEVK(F)** 
                 
                 4 
                 1.02 
                 1.52 
                 2.3 
                  4.62 
                  8.6 
               
               
                 2958.35 
                 (R)WQQGNVFSCSVMHEALHNHYTQK(S) 
                 5 
                 
                   0.88 
                 
                 
                   0.84 
                 
                 
                   1.61 
                 
                   2.88   
                   2.9   
               
               
                 2974.35 
                 (R)WQQGNVFSCSVMHEALHNHYTQK(S) 
                 5 
                 
                   0.72 
                 
                 1.59 
                 2.18 
                  5.01 
                 11 
               
            
           
           
               
               
               
               
               
               
            
               
                 Mean of the Observed Ratio 
                 1.04 
                 1.47 
                 2.09 
                  4.41 
                  9.38 
               
               
                 Expected Ratio 
                 1 
                 1.5 
                 2 
                  5 
                 10 
               
               
                 Standard Deviation 
                 0.04 
                 0.1 
                 0.19 
                  0.56 
                  1.2 
               
               
                 % Error 
                 4 
                 1.83 
                 4.38 
                 11.9 
                  6.25 
               
               
                   
               
               
                 In TABLE XIX, *indicates observed ratio values. Underlining indicates poor quality or overlapping peaks. These values were not included in the statistical calculation.  
               
            
           
         
       
     
     From these data, it was illustrated that the observed ratios closely reflect the expected ratios of light to heavy ICIER labeled peptides, especially when mass peaks that give very weak intensity or overlap with other mass peaks were excluded. The percentage error of quantitation using the ICIER approach is less than 12% for all ratios which is very accurate in contrast to densitometry. Furthermore, the ICIER approach is also capable of quantifying multiple proteins in a single sample, gel band or spot since the quantitation is based on peptides with known sequence identity. 
     From these data, it was also concluded that with the use of a mixture of light and heavy ICIER, an exact number of cysteine residues contained in each detected MS peak can be determined based on the presence or absence of the isotopically labeled pairs without extra sample manipulation (see TABLE XX). This additional information can be readily used with peptide masses for a more constrained peptide mass mapping to give confident protein identification. This is particularly useful when dealing with more than one protein in an analysis or only a limited number of mass peaks. 
     
       
         
           
               
             
               
                 TABLE XX 
               
             
            
               
                   
               
               
                 Identification of the exact number of cysteine residues in each 
               
               
                 MS peaks 
               
            
           
           
               
               
               
               
            
               
                 Experimental 
                 Exact Number 
                 Sequence of Cysteine-Containing 
                   
               
               
                 Mass (Da) 
                 of Cysteines 
                 Peptides Derived from CTLA4-IgG: 
                 SEQ ID NO: 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 587.1578 
                 0 
                   
                   
               
               
                 951.2411 
                 0 
               
               
                 1286.6826 
                 0 
               
               
                 1318.6902 
                 1—light 
                 (K)NQVSLTC*LVK(G) 
                 1 
               
               
                 1325.6597 
                 1—heavy 
                 (K)NQVSLTC**LVK(G) 
                 1 
               
               
                 1344.7691 
                 1—light 
                 (R)AM*DTGLYIC*K(V) 
                 2 
               
               
                 1351.6682 
                 1—heavy 
                 (R)AM*DTGLYIC**K(V) 
                 2 
               
               
                 1481.7472 
                 0 
               
               
                 1642.8055 
                 1—light 
                 (R)GIASFVC*EYASPGK(A) 
                 3 
               
               
                 1649.9140 
                 1—heavy 
                 (R)GIASFVC**EYASPGK(A) 
                 3 
               
               
                 1677.6275 
                 0 
               
               
                 1689.7607 
                 0 
               
               
                 1807.8651 
                 0 
               
               
                 1872.8749 
                 0 
               
               
                 2296.0488 
                 1—light 
                 (R)TPEVTC*VVVDVSHEDPEVK(F) 
                 4 
               
               
                 2303.1326 
                 1—heavy 
                 (R)TPEVTC**VVVDVSHEDPEVK(F) 
                 4 
               
               
                 2958.8857 
                 1—light 
                 (R)WQQGNVFSC*SVMHEALHNHYTQK(S) 
                 5 
               
               
                 2965.5758 
                 1—heavy 
                 (R)WQQGNVFSC**SVMHEALHNHYTQK(S) 
                 5 
               
               
                 2974.3697 
                 1—light 
                 (R)WQQGNVFSC*SVM*HEALHNHYTQK(S) 
                 5 
               
               
                 2981.1270 
                 1—heavy 
                 (R)WQQGNVFSC**SVM*HEALHNHYTQK(S) 
                 5 
               
               
                 3336.6515 
                 0 
               
               
                   
               
               
                 Abbreviations: C*, cysteine residue labeled by light ICIER; C**, cysteine residue labeled by heavy ICIER; M*, oxidized methionine.  
               
            
           
         
       
     
     All publications cited in this specification are incorporated by reference herein. While the invention has been described with reference to a particularly preferred embodiment, it will be appreciated that modifications can be made without departing from the spirit of the invention. Such modifications are intended to fall within the scope of the appended claims.