Effects of peptide acetylation and dimethylation on electrospray ionization efficiency

Peptide acetylation and dimethylation have been widely used to derivatize primary amino groups (peptide N‐termini and the ε‐amino group of lysines) for chemical isotope labeling of quantitative proteomics or for affinity tag labeling for selection and enrichment of labeled peptides. However, peptide acetylation results in signal suppression during electrospray ionization (ESI) due to charge neutralization. In contrast, dimethylated peptides show increased ionization efficiency after derivatization, since dimethylation increases hydrophobicity and maintains a positive charge on the peptide under common LC conditions. In this study, we quantitatively compared the ESI efficiencies of acetylated and dimethylated model peptides and tryptic peptides of BSA. Dimethylated peptides showed higher ionization efficiency than acetylated peptides for both model peptides and tryptic BSA peptides. At the proteome level, peptide dimethylation led to better protein identification than peptide acetylation when tryptic peptides of mouse brain lysate were analyzed with LC‐ESI‐MS/MS. These results demonstrate that dimethylation of tryptic peptides enhanced ESI efficiency and provided up to two‐fold improved protein identification sensitivity in comparison with acetylation. Copyright © 2016 John Wiley & Sons, Ltd.     

Quantification of peptides using N‐terminal isotope coding and C‐terminal derivatization for sensitive analysis by micro liquid chromatography‐tandem mass spectrometry

Stable isotope‐coding coupled with mass spectrometry is a popular method for quantitative proteomics and peptide quantification. However, the efficiency of the derivatization reaction at a particular functional group, especially in complex structures, can affect accuracy. Here, we present a dual functional‐group derivatization of bioactive peptides followed by micro liquid chromatography‐tandem mass spectrometry (LC‐MS/MS). By separating the sensitivity‐enhancement and isotope‐coding derivatization reactions, suitable chemistries can be chosen. The peptide amino groups were reductively alkylated with acetaldehyde or acetaldehyde‐d₄ to afford N‐alkylated products with different masses. This process is simple, quick and high‐yield, and accurate comparative analysis can be achieved for the mass‐differentiated peptides. Then, the carboxyl groups were derivatized with 1‐(2‐pyrimidinyl)piperazine to increase MS/MS sensitivity. Angiotensins I–IV, bradykinin and neurotensin were analyzed after online solid phase extraction by micro LC‐MS/MS. In all instances, a greater than 17‐fold increase in sensitivity was achieved, compared with the analyses of the underivatized peptides. Furthermore, the values obtained from the present method were in agreement with the result from isotope dilution quantification using isotopically labeled angiotensin I [Asp‐Arg‐(Val‐d₈)‐Tyr‐Ile‐His‐Pro‐(Phe‐d₈)‐His‐Leu]. Copyright © 2016 John Wiley & Sons, Ltd.     

Characterization of the dehydration products due to thermal decomposition of peptides by liquid chromatography‐tandem mass spectrometry

Thermal decomposition (TD) of proteins is being investigated as a rapid digestion step for bottom‐up proteomics. Mass spectrometry (MS) analyses of the TD products of simple peptides and intact proteins have revealed several nonvolatile products at masses lower than the precursor biomolecule (M). In addition to products stemming from site‐specific cleavages, many signals are also observed at a corresponding M‐18, most likely because of dehydration (M‐H₂O) during the heating process. Understanding the structural nature of the water loss product is important in establishing the utility of their tandem mass spectra (collision‐induced dissociation) in determining the precursor ion amino acid sequence in a bottom‐up proteomic workflow. Dehydration of a peptide can take place from a variety of sources including side chain groups, C‐terminus, and/or intramolecular cyclization (C to N‐terminus cyclization). In this work, liquid chromatography‐tandem MS (LC‐MS/MS) and a series of standard peptides (angiotensin II, DRVYIHPF and its cyclic analog) are implemented to decipher the structure of the TD dehydration product. In addition, a derivatization strategy incorporating N‐terminus acetylation was developed that allowed the direct comparison of tandem mass spectra of standard cyclic peptides with those resulting from the TD process, thus eliminating any ambiguity from the direct comparison of their mass spectra (due to gas‐phase cyclization of b‐ions, which can result in sequence scrambling of the precursor ion). Results from these investigations indicated that peptide dehydrated TD products were mostly linear in nature, and water loss was favored from the C‐terminus carboxyl group or, when present, the aspartic acid side chain. Given the predictable nature of the formation of TD dehydration products, their MS/MS analysis can be of utility in providing complementary and confirmatory sequence information of the precursor peptide. Copyright © 2015 John Wiley & Sons, Ltd.     

Proteins from Erwinia asparaginase Erwinase® and E. coli asparaginase 2 MEDAC® for treatment of human leukemia,show a multitude of modifications for which the consequences are completely unclear

L ‐Asparaginase from Erwinia chrysanthemi (ASPG_ERWCH; UniProtKB accession number P06608 (Erwinase^®)) and L ‐asparaginase 2 from Escherichia coli (ASPG2_ECOLI; UniProtKB accession number P00805 (Medac^®)), both L ‐asparagine amidohydrolases, are widely used for the treatment of acute lymphoblastic leukemia. A series of serious side effects have been reported and this warrants studies into the protein chemistry of the medical products sold. Mass spectrometry (MS) data on ASPG_ERWCH and ASPG2_ECOLI have not been published so far and herein a gel‐based proteomics study was performed to provide information about sequence and modifications of the commercially available medical products. ASPG_ERWCH and ASPG2_ECOLI were applied onto two‐dimensional gel electrophoresis, spots were in‐gel digested with several proteases and resulting peptides and protein modifications were analysed by nano‐ESI‐LC‐MS/MS. Four spots were observed for ASPG_ERWCH, six spots were observed for ASPG2_ECOLI and the identified proteins showed high sequence coverage without sequence conflicts. Several protein modifications including technical and posttranslational modifications were demonstrated. Protein modifications are known to change physicochemical, immunochemical, biological and pharmacological properties and results from this work may challenge re‐designing of the product including possible removal of the modifications by the manufacturer because it is not known whether they are contributing to the serious adverse effects of the protein drug.     

A matrix-assisted laser desorption/ionization compatible reagent for tagging tryptophan residues

Chemical tagging of amino acids is an important tool in proteomics analysis, and has been used to introduce isotope labels and mass defect labels into proteolytic peptides by derivatization of cysteine or lysine residues. Here, we present a new reagent with chemical specificity for tryptophan residues. Previously, 2-nitrobenzenesulfenyl chloride has been used as a highly specific reagent for labeling tryptophan residues. We show that this tag undergoes UV dissociation during matrix assisted laser desorption/ionization (MALDI). The multiplicity of photofragments increases the difficulty of characterizing the derivatization products. To overcome this problem, we have synthesized a new reagent, 2-(trifluoromethyl)benzenesulfenyl chloride, which is shown to react quantitatively with tryptophan in peptides and proteins. Most significantly, it exhibits high photostability in MALDI-Fourier transform mass spectrometry analyses.     

Photodissociation of Charge Tagged Peptides

Tris(2,4,6-trimethoxyphenyl) phosphonium acetyl (TMPP-Ac) was previously introduced to improve the mass spectrometric sequence analysis of peptides by fixing a permanent charge at the N-termini. However, peptides containing arginine residues did not fragment efficiently after TMPP-Ac modification. In this work, we combine charge derivatization with photodissociation. The fragmentation of TMPP-derivatized peptides is greatly improved and a series of N-terminal fragments is generated with complete sequence information. Arginine has a special effect on the fragmentation of the TMPP tagged peptides when it is the N-terminal peptide residue. Theoretical and experimental results suggest that this is due to hydrogen transfer from the charged N-terminus to the hydrogen-deficient peptide sequence.     

Pyrylium‐based dye and charge tagging in proteomics

The pyrylium group is a selective reagent for ε‐amino groups in proteins. In particular, for fluorescence labeling, a number of advantages over traditional N‐hydroxysuccinimidyl ester chemistry were recognized such as the rapid prestaining procedure. Here, we have investigated the labeling reaction for the fluorogenic pyrylium dye Py‐1 using liquid chromatography coupled to MS with the aim of determining its specificity and possible side products. Peptides containing no, one, and two lysine residue and a choice of no or one cysteine residue were labeled with Py‐1 at yields > 30%. Gas phase fragmentation proved both labeling of lysine residues as well as that of the N‐terminus also in peptides that contained a lysine residue. Evidence for cysteine labeling was not found, but several other products were detected such as the results of rearrangements with adjacent acidic amino acids. Apart from the use as a fluorogenic label, Py‐1 recommends itself for N‐terminal charge tagging as alternative to the commonly used quaternary ammonium salts. Predominantly a‐ and b‐type ion series were observed for N‐terminally labeled peptides. Further applications include chromophore tagging since the labeled product is not only fluorescent but also colored red.     

氨基酸和多肽在碱性硅胶载体上的固相衍生研究

为进行复杂体系中痕量生理活性物质 (如氨基酸和多肽等 )的高灵敏度分析 ,往往需要对其进行柱前或柱后的荧光衍生 -高效液相色谱或毛细管电泳分析 [1] .在一个存在着竞争反应的体系中 ,为保证样品有足够的反应产率 ,往往需使衍生试剂过量很多 ,这就使得衍生后的样品中必然含有高浓度的衍生试剂及其水解后形成的副产物 ,从而大大地干扰了分离与分析 .为解决这一问题 ,通常可采取溶剂萃取[2～ 5] 或加入 1 -金刚烷胺 [6 ,7] 或羟胺 [8,9] 等方法除去过量试剂 .但这些额外的处理使衍生方法更加烦琐 ,有时还导致收率的降低 .也有使用固相化的衍…     

MeCAT—new iodoacetamide reagents for metal labeling of proteins and peptides

Besides protein identification via mass spectrometric methods, protein and peptide quantification has become more and more important in order to tackle biological questions. Methods like differential gel electrophoresis or enzyme-linked immunosorbent assays have been used to assess protein concentrations, while stable isotope labeling methods are also well established in quantitative proteomics. Recently, we developed metal-coded affinity tagging (MeCAT) as an alternative for accurate and sensitive quantification of peptides and proteins. In addition to absolute quantification via inductively coupled plasma mass spectrometry, MeCAT also enables sequence analysis via electrospray ionization tandem mass spectrometry. In the current study, we developed a new labeling approach utilizing an iodoacetamide MeCAT reagent (MeCAT-IA). The MeCAT-IA approach shows distinct advantages over the previously used MeCAT with maleinimide reactivity such as higher labeling efficiency and the lack of diastereomer formation during labeling. Here, we present a careful characterization of this new method focusing on the labeling process, which yields complete tagging with an excess of reagent of 1.6 to 1, less complex chromatographic behavior, and fragmentation characteristics of the tagged peptides using the iodoacetamide MeCAT reagent.     

Quantitative determination of amphetamine in plasma using negative ion chemical ionization GC‐MS of o‐(pentafluorobenzyl‐oxycarbonyl)‐2,3,4,5‐tetrafluorobenzoyl derivatives

Quantitative determination of amphetamine in plasma by the use of a novel electrophoric derivatization reagent, o‐(pentafluorobenzyloxycarbonyl)‐2,3,4,5‐tetrafluorobenzoyl chloride is described. Amphetamine can be quantitatively measured down to 49 pg/mL plasma using only 250 μL of sample due to the extraordinary sensitivity of the derivatives under negative ion chemical ionization MS. Plasma samples were made alkaline with carbonate buffer and treated with n‐hexane and reagent solution for 20 min, which, after concentration was measured by negative ion chemical ionization GC‐MS. The method is rapid as extraction and derivatization occur in one single step. [²H₅]‐Amphetamine was used as an internal standard. Validation data are given to demonstrate the usefulness of the assay, including specificity, linearity, accuracy and precision, benchtop stability, freeze–thaw stability, autosampler stability, aliquot analysis, and prospective analytical batch size accuracy.     

The Coordination of NiII and CuII Ions to the Polyhistidyl Motif of Hpn Protein: Is It as Strong as We Think?

Hpn, one of Helicobacter pylori′s nickel‐accessory proteins, is an amazingly peculiar protein: Almost half of its sequence consists of polyhistidyl (poly‐His) residues. Herein, we try to understand the origin of this naturally occurring sequence, thereby shedding some light on the bioinorganic chemistry of Hpn′s numerous poly‐His repeats. By using potentiometric, mass spectrometric, and various spectroscopic techniques, we studied the Ni^II‐ and Cu^II complexes of the wild‐type Ac‐THHHHYHGG‐NH₂ fragment of Hpn and of its six analogues, in which consecutive residues (His or Tyr) were replaced by Ala (Ala‐substitution or Ala‐scan approaches), thereby resulting in Ac‐TAHHHYHGG‐NH₂, Ac‐THAHHYHGG‐NH₂, Ac‐THHAHYHGG‐NH₂, Ac‐THHHAYHGG‐NH₂, Ac‐THHHHAHGG‐NH₂, and Ac‐THHHHYAGG‐NH₂ peptides. We found that the His4 residue is critical for both Ni^II‐ and Cu^II‐ion binding and the effectiveness of binding varies even if the substituted amino acid does not take part in the direct binding interactions.     

Introducing the Petasis Reaction for Late‐Stage Multicomponent Diversification,Labeling, and Stapling of Peptides

For the first time, the Petasis (borono‐Mannich) reaction is employed for the multicomponent labeling and stapling of peptides. The report includes the solid‐phase derivatization of peptides at the N‐terminus, Lys, and N^?‐MeLys side‐chains by an on‐resin Petasis reaction with variation of the carbonyl and boronic acid components. Peptides were simultaneously functionalized with aryl/vinyl substituents bearing fluorescent/affinity tags and oxo components such as dihydroxyacetone, glyceraldehyde, glyoxylic acid, and aldoses, thus encompassing a powerful complexity‐generating approach without changing the charge of the peptides. The multicomponent stapling was conducted in solution by linking N^?‐MeLys or Orn side‐chains, positioned at i, i+7 and i, i+4, with aryl tethers, while hydroxy carbonyl moieties were introduced as exocyclic fragments. The good efficiency and diversity oriented character of these methods show prospects for peptide drug discovery and chemical biology.     

Introducing the Petasis Reaction for Late‐Stage Multicomponent Diversification,Labeling, and Stapling of Peptides

For the first time, the Petasis (borono‐Mannich) reaction is employed for the multicomponent labeling and stapling of peptides. The report includes the solid‐phase derivatization of peptides at the N‐terminus, Lys, and N^?‐MeLys side‐chains by an on‐resin Petasis reaction with variation of the carbonyl and boronic acid components. Peptides were simultaneously functionalized with aryl/vinyl substituents bearing fluorescent/affinity tags and oxo components such as dihydroxyacetone, glyceraldehyde, glyoxylic acid, and aldoses, thus encompassing a powerful complexity‐generating approach without changing the charge of the peptides. The multicomponent stapling was conducted in solution by linking N^?‐MeLys or Orn side‐chains, positioned at i, i+7 and i, i+4, with aryl tethers, while hydroxy carbonyl moieties were introduced as exocyclic fragments. The good efficiency and diversity oriented character of these methods show prospects for peptide drug discovery and chemical biology.     

A new fluorescent derivatization reagent and its application to free fatty acid analysis in pomegranate samples using HPLC with fluorescence detection

A new fluorescent labeling reagent has been developed for the determination of fatty acids (FAs) by HPLC with fluorescence detection. The derivatization conditions including the amount of derivatization reagent, temperature, and type of catalyst were investigated, the results indicated that the reaction proceeded within 30 min at 90°C in the presence of K₂CO₃ catalyst. The maximal yield was obtained with a four‐ to fivefold molar reagent excess. The derivatives exhibited strong fluorescence with an excitation maximum at λ_ex = 245 nm and an emission maximum at λ_em = 410 nm. Twenty‐five FA derivatives were well separated by RP‐HPLC on a Hypersil BDS C₈ column in combination with gradient elution. All FAs were found to give excellent linear responses with correlation coefficients >0.9992. The method gave a low LOQ of 0.85–5.5 ng/mL (S/N of 10). The developed method was employed to analyze free FAs (FFAs) composition in pomegranate samples without any purification. FFAs in samples were doubly identified by HPLC retention time and protonated molecular ion corresponding to m/z [M+H]⁺. This newly developed method allows a highly sensitive determination of trace FFAs from pomegranate and other foodstuffs.     

3‐(2‐Bromoacetamido)‐N‐(9‐ethyl‐9H)‐carbazol fluorescent probe and its application for the determination of thiophenols in rubber products by HPLC with fluorescence detection and atmospheric chemical ionization mass spectrometry identification

A rapid, sensitive, and selective precolumn derivatization method for the simultaneous determination of eight thiophenols using 3‐(2‐bromoacetamido)‐N‐(9‐ethyl‐9H )‐carbazol as a labeling reagent by high‐performance liquid chromatography with fluorescence detection has been developed. The labeling reagent reacted with thiophenols at 50°C for 50 min in aqueous acetonitrile in the presence of borate buffer (0.10 mol/L, pH 11.2) to give high yields of thiophenol derivatives. The derivatives were identified by online postcolumn mass spectrometry. The collision‐induced dissociation spectra for thiophenol derivatives gave the corresponding specific fragment ions at m/z 251.3, 223.3, 210.9, 195.8, and 181.9. At the same time, derivatives exhibited intense fluorescence with an excitation maximum at λ_ex = 276 nm and an emission maximum at λ_em = 385 nm. Excellent linear responses were observed for all analytes over the range of 0.033–6.66 μmol/L with correlation coefficients of more than 0.9997. Detection limits were in the range of 0.94–5.77 μg/L with relative standard deviations of less than 4.54%. The feasibility of derivatization allowed the development of a rapid and highly sensitive method for the quantitative analysis of trace levels of thiophenols from some rubber products. The average recoveries (n = 3) were in the range of 87.21–101.12%.     

Reactivity of Tyr–Leu and Leu–Tyr dipeptides: identification of oxidation products by liquid chromatography–tandem mass spectrometry

The exposure of peptides and proteins to reactive hydroxyl radicals results in covalent modifications of amino acid side‐chains and protein backbone. In this study we have investigated the oxidation the isomeric peptides tyrosine–leucine (YL) and leucine–tyrosine (LY), by the hydroxyl radical formed under Fenton reaction (Fe²⁺/H₂O₂). Through mass spectrometry (MS), high‐performance liquid chromatography (HPLC‐MS) and electrospray tandem mass spectrometry (HPLC‐MSⁿ) measurements, we have identified and characterized the oxidation products of these two dipeptides. This approach allowed observing and identifying a wide variety of oxidation products, including isomeric forms of the oxidized dipeptides. We detected oxidation products with 1, 2, 3 and 4 oxygen atoms for both peptides; however, oxidation products with 5 oxygen atoms were only present in LY. LY dipeptide oxidation leads to more isomers with 1 and 2 oxygen atoms than YL (3 vs 5 and 4 vs 5, respectively). Formation of the peroxy group occurred preferentially in the C‐terminal residue. We have also detected oxidation products with double bonds or keto groups, dimers (YL–YL and LY–LY) and other products as a result of cross‐linking. Both amino acids in the dipeptides were oxidized although the peptides showed different oxidation products. Also, amino acid residues have shown different oxidation products depending on the relative position on the dipeptide. Results suggest that amino acids in the C‐terminal position are more prone to oxidation. Copyright © 2009 John Wiley & Sons, Ltd.     

A method for N-terminal de novo sequencing of Nα-blocked proteins by mass spectrometry

A method for de novo sequencing of N(α)-blocked proteins by mass spectrometry (MS) is presented. The approach consists of enzymatic digestion of N(α)-blocked protein, recovery of N-terminal peptide by depletion of non-N-terminal peptides from the digest pool, and selective derivatization of a C-terminal α-carboxyl group of isolated N-terminal peptide. The C-terminal α-carboxyl group of the N-terminal peptide was selectively derivatized with 3-aminopropyl-tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-propylamine), according to oxazolone chemistry. The reagent TMPP-propylamine was designed to facilitate sequence analysis with MALDI-MS by mass- and charge-tagging. All of the identities and N-terminal sequences of two N(α)-acetylated proteins (rabbit phosphorylase b and bovine calmodulin) and human orexin A, which has pyroglutamic acid at the N-terminus, were successfully analyzed by allowing for the y-type ions almost exclusively.     

Sub-nanogram detection of dihydroartemisinin after chemical derivatization with diacetyldihydrofluorescein followed by high-performance liquid chromatography and UV absorption

Summary The use of diacetyldihydrofluorescein (DADF) for derivatization of dihydroartemisinin (dihydroqinghaosu, DHQHS) is proposed. The reaction between DHQHS and this reagent in the presence of 4-dimethylaminopyridine (DMAP) and N,N′-dicyclohexylcarbodiimide (DCC) was complete in 8 hours at room temperature giving about 80 per cent theoretical yield. The derivative showed intense UV absorption, thus providing a sensitivity of 0.1 nanogram by UV detection after column separation. The influences of the ratio of the reagents, reaction temperature, chromatographic conditions and the extent of detection linearity were investigated. The reaction gave consistent results and chromatographic separation was not affected by an excess of the reagent or side products.     

Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides

In this work, a non‐natural amino acid, H‐propargylglycine‐OH (Pra), is chosen to examine the side‐chain effect on the backbone conformation of small peptides. The conformations of two synthesized Pra‐containing tripeptides, Ac‐Pra‐Pra‐NH₂ (PPTP) and Ac‐Pra‐Ala‐NH₂ (PATP), are examined by infrared (IR) spectroscopy in combination with molecular dynamics (MD) simulations and quantum chemical computations. By analyzing the joint distributions of backbone torsional angles, several significant conformations can be identified for the two tripeptides solvated in D₂O. At room temperature, 44 % of PPTP exists in the α‐α conformation and 33 % of PATP exists in the α‐polyproline‐II conformation. Larger structural inhomogeneity is seen in both cases by MD simulations at elevated temperatures. Thus even a small side chain, such as the propargyl group can significantly alter the peptide backbone conformations. The results suggest that there is no overwhelming conformational propensity of the Pra residue in short peptides. IR spectra simulated in the amide‐I region using two different methods, reasonably reproduce the experimental IR spectra and their temperature dependence.