The significance of monoisotopic and carbon-13 isobars for the identification of a 19-component dodecapeptide library by positive ion electrospray Fourier transform ion cyclotron resonance mass spectrometry

Accurate mass as a bioinformatic parameter in data-to-knowledge conversion: Fourier transform ion cyclotron resonance mass spectrometry for peptide de novo sequencing

With the availability of ultra-precise mass spectrometric biomolecular data, the accurate mass is becoming a physical quantity of high interest for bioinformatics tools and strategies. Fourier transform ion cyclotron resonance mass spectrometry with electrospray ionization or matrix-assisted laser desorption/ionization sources now allows the easy determination of amino acid composition of medium size, unknown peptides when employing combinatorial calculation of hypothetical parent and fragment ion masses. This new method, which in a second step, allows the reliable de-novo sequencing of completely unknown peptides ["composition-based sequencing (CBS)"(1)] appears to open a wide new field of bioanalytical investigation. It has been shown that even unspecifically cleaved proteins can be identified easily and reliably when accurate mass evaluation is combined with protein database search tools.(2) It is quite clear that, while the nominal mass of a peptide has obviously no useful correlation to biomolecular structure, the accurate mass, instead, has a strong and direct correlation to structure that so far has not been exploited considerably by bioinformatic tools. It has already become obvious that accurate mass evaluation is going to become a central goal for bioinformatics strategies in the near future.(3-11) Strategies for extracting structural, and even functional, information out of accurate mass values of biomolecules still have to be developed. Examples and prospects of accurate mass evaluation in bioinformatics for the field of proteomics are outlined in the following.

Screening of Combinatorial Libraries for Substrate Preference by Mass Spectrometry

We present a rapid screening method for monitoring enzyme specificity using both combinatorial chemistry and mass spectrometry where, as an example, the substrate specificity of peptidylglycine alpha-amidating enzyme was determined and compared against a conventional quantitative technique. Whereas alternative methods for library screening are generally limited to certain enzymes and can present difficulties in the synthesis or derivatization of potential substrates, the approach we call chirality-based isotope labeling for a library of substrates (CHILLS) does not fall short to such limitations, since we exploit the inherent stereospecificity of enzymes to determine preferred substrates. Additionally, the CHILLS method generates accurate results, as compared to typical screening procedures that require tedious method development, because the synthesized library contains a structurally similar internal standard for each individual library component in order to quantitate the progress of enzymatic reactions.

De novo sequencing, peptide composition analysis, and composition-based sequencing: a new strategy employing accurate mass determination by fourier transform ion cyclotron resonance mass spectrometry

A new strategy is described for the determination of amino acid sequences of unknown peptides. Different from the well-known but often inefficient de novo sequencing approach, the new method is based on a two-step process. In the first step the amino acid composition of an unknown peptide is determined on the basis of accurate mass values of the peptide precursor ion and a small number of accurate fragment ion mass values, and, as in de novo sequencing, without employing protein database information or other pre-information. In the second step the sequence of the found amino acids of the peptide is determined by scoring the agreement between expected and observed fragment ion signals of the permuted sequences. It was found that the new approach is highly efficient if accurate mass values are available and that it easily outstrips common approaches of de novo sequencing being based on lower accuracies and detailed knowledge of fragmentation behavior. Simple permutation and calculation of all possible amino acid sequences, however, is only efficient if the composition is known or if possible compositions are at least reduced to a small list. The latter requires the highest possible instrumental mass accuracy, which is currently provided only by fourier transform ion cyclotron resonance mass spectrometry. The connection between mass accuracy and peptide composition variability is described and an example of peptide compositioning and composition-based sequencing is presented.

Theoretical and Experimental Prospects for Protein Identification Based Solely on Accurate Mass Measurement

We discuss the theoretical and experimental potential and limitations of protein identification by mass measurement of proteolytic peptides and database searching. For peptides differing in composition by one (or two or three) amino acids, a surprisingly high number turn out to have isomers: 10% (or 29% or 53%), considering the 20 common amino acids with equal relative abundance. Even if isomers differing by leucine/isoleucine are excluded, the latter numbers are 14% and 38%--those isomeric peptides cannot be distinguished based on mass alone, and tandem mass spectrometry and/or other additional constraints are needed. However, for nominally isobaric peptides, the mass accuracy and resolving power of broadband Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry theoretically and experimentally suffice to resolve virtually all peptide doublets differing by up to two amino acids--including the smallest mass difference of 3.4 mDa. We demonstrate experimental resolution of another pair of peptides differing by 11 mDa, even when present in a complex mixture of hundreds of other peptides.

Progress in liquid chromatography-mass spectrometry instrumentation and its impact on high-throughput screening

In the past 10 years, liquid chromatography-mass spectrometry (LC-MS) has rapidly matured to become a very powerful and useful analytical tool that is widely applied in many areas of chemistry, pharmaceutical sciences and biochemistry. In this paper, recent instrumental developments in LC-MS-related interfacing, ionization and mass analysis are reviewed from the perspective of the application of LC-MS in high-throughput screening of combinatorial libraries and the related high-throughput quantitative bioanalysis in early drug-discovery studies, such as early adsorption, distribution, metabolism and excretion studies.

Mass spectrometric analysis of combinatorial peptide libraries derived from the tandem repeat unit of MUC2 mucin

Four 19-member synthetic peptide libraries, based on the TX1TX2T epitope motif of the mucin-2 gastrointestinal glycoprotein (MUC2) and ranging in peptide length from dipeptides to 15-mers (XT, TXT, TQTXT and KVTPTPTPTGTQTXT), were synthesized by combinatorial solid phase peptide synthesis using the portioning-mixing combinatorial approach, and analysed by electrospray ionization mass spectrometry at different (1000-10000) resolutions. Most of the components of the individual libraries could be easily identified in a single-stage molecular mass screening experiment. The resolving power of the instrument becomes an important factor above 800-1000 Da molecular mass, when predominantly multiply charged molecular ions are formed. Approaches to the identification of isobars (glutamine/lysine), isomers leucine/isoleucine) and sequence variations by tandem mass spectrometry, and/or by high-performance liquid chromatography-mass spectrometry are outlined.

Parallel high-throughput accurate mass measurement using a nine-channel multiplexed electrospray liquid chromatography ultraviolet time-of-flight mass spectrometry system

A nine-channel multiplexed electrospray (MUX) liquid chromatography ultraviolet time-of-flight mass spectrometry (LC/UV/TOFMS) system has been used to simultaneously measure accurate masses of eluting components from eight parallel gradient LC columns. Accuracies better than 5 and 10 ppm were achieved for 50 and 80% of samples, respectively, from a single batch analysis of ten plates (960 samples) of a Fmoc-Asp(OtBu)-OH and reserpine mixture. Combinatorial library compounds were analyzed using this parallel high-throughput system in both positive and negative modes to rigorously verify expected products and identify side products. A mass accuracy of 10 ppm root mean square (RMS) is routinely obtained for combinatorial library samples from this high-throughput accurate mass LC/MS system followed by automated data processing. This mass accuracy is critical in revealing combinatorial synthesis problems that would be missed by unit mass measurement.

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry to reveal the substrate specificity of the peptidyl-cysteine decarboxylase EpiD

The microbial flavoenzyme EpiD catalyzes the oxidative decarboxylation of peptidyl-cysteines to peptidyl-aminoenethiols. These unusual C-terminally modified peptides are intermediates in the biosynthesis of the tetracyclic peptide antibiotic epidermin, which belongs to the lantibiotics family. The peptide SFNSYCC represents the C-terminal partial sequence of the natural precursor peptide EpiA. EpiA is posttranslationally modified to form finally the lantibiotic epidermin. The substrate specificity of EpiD was investigated using high-resolution mass spectrometry and the heptapeptide library SFNSXCC. The enzymatic conversion of particular peptides can be observed by a mass loss of m/z 46. In contrast to the previously used triple quadrupole instrument, electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) was able to resolve and detect all precursor and converted peptides with identical nominal masses in a single measurement, avoiding the necessity to investigate single peptides. Furthermore, a new substrate SFNSCCC of the enzyme EpiD was detected within the reaction mixture.

Characterisation of combinatorial libraries of mucin-2 antigen peptides by high-resolution mass spectrometry

An epitope motif, TX(1)TX(2)T, of mucin-2 glycoprotein was identified by means of a mucin-2-specific monoclonal antibody, mAb 994, raised against a synthetic mucin-derived 15-mer peptide conjugate. For determination of the epitope sequence recognised with highest affinity by mAb 994, a combinatorial approach was applied using the portioning-mixing technique excluding Cys. Antibody binding of libraries was most profound when Gln was at the X(1) position. Analytical characterisation of the TQTX(2)T library was conducted by amino acid analysis and matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) and electrospray ionisation Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometric methods. Control libraries were prepared by mixing 19 individual peptides corresponding to the TQTX(2)T sequence. Thus, mixtures of 6, 10 and 19 pentapeptides were analysed and compared with the combinatorial mixture. MALDI-TOFMS was able to detect only partially the components in the 6- and 10-member mixtures, but failed to characterise a more complex 19-member mixture. In contrast, ESI-FTICRMS resolved all mixtures of higher complexity and provided direct identification at monoisotopic resolution, such as for a peptide library containing 'isobaric' lysine and glutamine (Delta m = 0.0364 Da). The results of this study suggest that ESI-FTICRMS is a powerful tool for characterisation of combinatorial peptide libraries of higher complexity.

Broadband detection electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry to reveal enzymatically and chemically induced deamidation reactions within peptides

Among the numerous forms of chemical degradation of peptides or proteins, deamidation is one of the alterations observed most frequently. In this irreversible reaction, a glutamine or an asparagine side chain is hydrolyzed to glutamic acid or aspartic acid, respectively (conversion of NH2 to OH). Besides its influence in the deterioration of biotechnological and food products, deamidation represents a defined posttranslational modification reaction with respect to proteomics. Here mass spectrometric techniques play a leading role in determining posttranslational modifications. However, not all mass spectrometers are able to resolve signal differences of 0.0193 Da (mass difference of 12CO vs 13CNH) for singly charged molecules, the mass difference between the first isotopic signal of an asparagine/glutamine-containing peptide and the monoisotopic signal of the corresponding partially deamidated aspartate/glutamate derivative. To detect partial deamidation within peptides, advantage has been taken of the ability of Fourier transform ion cyclotron resonance mass spectrometry to perform very high mass resolution. In this work, we investigated up to triply charged ions produced by electrospray ionization using direct infusion. Although the special heterodyne detection mode enables higher mass resolution than the routinely used broadband detection, often only a small mass window can be investigated. Using broadband detection, we were able to resolve ions with a difference of m/z 0.0064 to detect partially deamidated peptides formed either enzymatically or under acidic and basic conditions.

The synthesis of a prodrug of doxorubicin designed to provide reduced systemic toxicity and greater target efficacy

Doxorubicin (Dox) can provide some stabilization in prostate cancer; however, its use is limited because of systemic toxicities, primarily cardiotoxicity and immunosuppression. The administration of a prodrug of doxorubicin, designed to permit selective activation by the tumor, would reduce general systemic exposure to the active drug and would thereby increase the therapeutic index. Prostate specific antigen (PSA) is a serine protease with chymotrypsin-like activity that is a member of the kallikrein gene family. PSA's putative physiological role is the liquefaction of semen by virtue of its ability to cleave the seminal fluid proteins semenogelins I and II. Serum PSA levels have been found to correlate well with the number of malignant prostate cells. The use of a prodrug which is cleaved by the enzyme PSA in the prostate should in principle produce high localized concentrations of the cytotoxic agent at the tumor site while limiting systemic exposure to the active drug. Cleavage maps following PSA treatment of human semenogelin were constructed. Systematic modification of the amino acid residues flanking the primary cleavage site led to the synthesis of a series of short peptides which were efficiently hydrolyzed by PSA. Subsequent coupling of selected peptides to doxorubicin provided a series of doxorubicin-peptide conjugates which were evaluated in vitro and in vivo as targeted prodrugs for PSA-secreting tumor cells. From these studies we selected Glutaryl-Hyp-Ala-Ser-Chg-Gln-Ser-Leu-Dox, 27, as the peptide-doxorubicin conjugate with the best profile of physical and biological properties. Compound 27 has a greater than 20-fold selectivity against human prostate PSA-secreting LNCaP cells relative to the non-PSA-secreting DuPRO cell line. In nude mouse xenograft studies, 27 reduced PSA levels by 95% and tumor weight by 87% at a dose below its MTD. Both doxorubicin and Leu-Dox (13) were ineffective in reducing circulating PSA and tumor burden at their maximum tolerated doses. On the basis of these results, we selected 27 for further study to assess its ability to inhibit human prostate cancer cell growth and tumorigenesis.

High-resolution analysis of a 144-membered pyrazole library from combinatorial solid phase synthesis by using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry

A compound library consisting of 144 pyrazole carboxylic acids and six sublibraries consisting of 24 components was analysed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The library was synthesised by the split-mix method and investigated by direct infusion analysis by which 134 compounds were detected. FTICR-MS is predestined for the direct characterisation of complex compound libraries because of its outstanding mass resolution and mass accuracy. However, discrimination within the electrospray ionisation process sometimes leads to signal suppression and thus to misinterpretation of the synthetic results. Using micro-HPLC/MS we were able to assign all 144 compounds including all pairs of isobaric pyrazoles. We also show that, due to partial separation, FTICR-MS is indispensable for proper detection of co-eluting compounds.