Mass spectrometric identification of proteins and characterization of their post-translational modifications in proteome analysis

Do the complementarities of electrokinetic and chromatographic procedures represent the "Swiss knife" in proteomic investigation? An overview of the literature in the past decade

This report reviews the literature of the past decade dealing with the combination of electrokinetic and chromatographic strategies in the proteomic field. Aim of this article is to highlight how the application of complementary techniques may contribute to substantially improve protein identification. Several studies here considered demonstrate that exploring the combination of these approaches can be a strategy to enrich the extent of proteomic information achieved from a sample. The coupling of "top-down" and "bottom-up" proteomics may result in the generation of a hybrid analytical tool, very efficient not only for large-scale profiling of complex proteomes but also for studying specific subproteomes. The range of applications described, while evidencing a continuous boost in the imagination of researchers for developing new combinations of methods for protein separation, also underlines the adaptability of these techniques to a wide variety of samples. This report points out the general usefulness of combining different procedures for proteomic analysis, an approach that allows researchers to go deeper in the proteome of samples under investigation.

Multiplex Biomarker Approaches in Type 2 Diabetes Mellitus Research

Type 2 diabetes mellitus is a multifactorial condition resulting in high fasting blood glucose levels. Although its diagnosis is straightforward, there is not one set of biomarkers or drug targets that can be used for classification or personalized treatment of individuals who suffer from this condition. Instead, the application of multiplex methods incorporating a systems biology approach is essential in order to increase our understanding of this disease. This chapter reviews the state of the art in biomarker studies of human type 2 diabetes from a proteomic and metabolomic perspective. Our main focus was on biomarkers for disease prediction as these could lead to early intervention strategies for the best possible patient outcomes.

Stereochemical Sequence Ion Selectivity: Proline versus Pipecolic-acid-containing Protonated Peptides

Substitution of proline by pipecolic acid, the six-membered ring congener of proline, results in vastly different tandem mass spectra. The well-known proline effect is eliminated and amide bond cleavage C-terminal to pipecolic acid dominates instead. Why do these two ostensibly similar residues produce dramatically differing spectra? Recent evidence indicates that the proton affinities of these residues are similar, so are unlikely to explain the result [Raulfs et al., J. Am. Soc. Mass Spectrom. 25, 1705-1715 (2014)]. An additional hypothesis based on increased flexibility was also advocated. Here, we provide a computational investigation of the "pipecolic acid effect," to test this and other hypotheses to determine if theory can shed additional light on this fascinating result. Our calculations provide evidence for both the increased flexibility of pipecolic-acid-containing peptides, and structural changes in the transition structures necessary to produce the sequence ions. The most striking computational finding is inversion of the stereochemistry of the transition structures leading to "proline effect"-type amide bond fragmentation between the proline/pipecolic acid-congeners: R (proline) to S (pipecolic acid). Additionally, our calculations predict substantial stabilization of the amide bond cleavage barriers for the pipecolic acid congeners by reduction in deleterious steric interactions and provide evidence for the importance of experimental energy regime in rationalizing the spectra. Graphical Abstract ᅟ.

Proton Mobility in b₂ Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides

A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b2 ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b2 ion standards. We show that the position of the His residue does affect the identity of the subsequent b2 ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b2 ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting.

Proteomic analysis of 'Zaosu' pear (Pyrus bretschneideri Rehd.) and its early-maturing bud sport

Maturation of fruits involves a series of physiological, biochemical, and organoleptic changes that eventually make fleshy fruits attractive, palatable, and nutritional. In order to understand the mature mechanism of the early-maturing bud sport of 'Zaosu' pear, we analyzed the differences of proteome expression between the both pears in different mature stages by the methods of a combination of two-dimensional electrophoresis (2-DE) and matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. Seventy-five differential expressed protein spots (p<0.05) were obtained between 'Zaosu' pear and its early-maturing bud sport, but only sixty-eight were demonstratively identified in the database of NCBI and uniprot. The majority of proteins were linked to metabolism, energy, stress response/defense and cell structure. Additionally, our data confirmed an increase of proteins related to cell-wall modification, oxidative stress and pentose phosphate metabolism and a decrease of proteins related to photosynthesis and glycolysis during the development process of both pears, but all these proteins increased or decreased faster in the early-maturing bud sport. This comparative analysis between both pears showed that these proteins were closely associated with maturation and could provide more detailed characteristics of the maturation process of both pears.

Effect of the sarcosine residue on sequence scrambling in peptide b(5) ions

The effect of N-methylation on sequence scrambling in the fragmentation of b5 ions has been investigated by studying a variety of peptides containing sarcosine (N-methylglycine). The product ion mass spectra for the b5 ions derived from Sar-A-A-A-Y-A and Sar-A-A-Y-A-A show only minor signals for non-direct sequence ions the major fragmentation reactions occurring from the unrearranged structures. This is in contrast to the b5 ions where the Sar residue is replaced by Ala and sequence scrambling occurs. The b5 ion derived from Y-Sar-A-A-A-A shows a product ion mass spectrum essentially identical to the spectrum of the b5 ion derived from Sar-A-A-A-Y-A, indicating that in the former case macrocyclization has occurred but the macrocyclic form shows a strong preference to reopen to put the Sar residue in the N-terminal position. Similar results were obtained in the comparison of b5 ions derived from A-Sar-A-A-Y-A and Sar-A-A-Y-A-A. The product ion mass spectra of the MH(+) ions of Y-Sar-A-A-A-A and A-Sar-A-A-Y-A show substantial signals for non-direct sequence ions indicating that fragmentation of the MH(+) ions channels extensively through the respective b5 ions and further fragmentation of these species.

Survey of shotgun proteomics

Proteins provide the verbs to biology, and proteomics provides the nouns for their analytical and discovery-driven studies. The term proteomics was coined in the 1990s and deals with the protein complement of the genome-the proteome. Following the classical proteomics era, the development of new mass spectrometric methods for peptide analysis permitted the identification of proteins in peptide mixtures obtained by proteolytic digestion of complex samples, e.g., shotgun proteomics. Since its introduction, shotgun proteomics became the standard technique for the analysis of protein hydrolyzates in a high-throughput way. In this chapter, we provide a survey in shotgun proteomics highlighting instruments and techniques used in modern second and third proteomics generation.

Non-direct sequence ions in the tandem mass spectrometry of protonated peptide amides--an energy-resolved study

The fragmentation reactions of the MH(+) ions of Leu-enkephalin amide and a variety of heptapeptide amides have been studied in detail as a function of collision energy using a QqToF beam type mass spectrometer. The initial fragmentation of the protonated amides involves primarily formation of bn ions, including significant loss of NH3 from the MH(+) ions. Further fragmentation of these bn ions occurs following macrocyclization/ring opening leading in many cases to bn ions with permuted sequences and, thus, to formation of non-direct sequence ions. The importance of these non-direct sequence ions increases markedly with increasing collision energy, making peptide sequence determination difficult, if not impossible, at higher collision energies.

Fragmentation reactions of methionine-containing protonated octapeptides and fragment ions therefrom: an energy-resolved study

The fragmentation reactions of the MH(+) ions as well as the b7, a7, and a7* ions derived therefrom have been studied in detail for the octapeptides MAAAAAAA, AAMAAAAA, AAAAMAAA, and AAAAAAMA. Ionization was by electrospray using a QqToF mass spectrometer, which allowed a study of the evolution of the fragmentation channels as a function of the collision energy. Not surprisingly, the product ion mass spectra for the b7 ions are independent of the original precursor sequence, indicating macrocyclization and reopening to the same mixture of protonated oxazolones prior to fragmentation. The results show that this sequence scrambling results in a distinct preference to place the Met residue in the C-terminal position of the protonated oxazolones. The a7 and a7* ions also produce product ion mass spectra independent of the original peptide sequence. The results for the a7 ions indicate that fragmentation occurs primarily from an amide structure analogous to that observed for a4 ions (Bythell et al. in J Am Chem Soc 132:14766-14779, 2010). Clearly, the rearrangement reaction they have proposed applies equally well to an ions as large as a7. The major fragmentation modes of the MH(+) ions at low collision energies produce b7, b6, and b5 ions. As the collision energy is increased further fragmentation of these primary products produces, in part, non-direct sequence ions, which become prominent at lower m/z values, particularly for the peptides with the Met residue near the N-terminus.

Optimal single-embryo mass spectrometry fingerprinting

In pre-implantation embryos, lipids play key roles in determining viability, cryopreservation and implantation properties, but often their analysis is analytically challenging because of the few picograms of analytes present in each of them. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) allows obtaining individual phospholipid profiles of these microscopic organisms. This technique is sensitive enough to enable analysis of individual intact embryos and monitoring the changes in membrane lipid composition in the early stages of development serving as screening method for studies of biology and biotechnologies of reproduction. This article introduces an improved, more comprehensive MALDI-MS lipid fingerprinting approach that considerably increases the lipid information obtained from a single embryo. Using bovine embryos as a biological model, we have also tested optimal sample storage and handling conditions before the MALDI-MS analysis. Improved information at the molecular level is provided by the use of a binary matrix that enables phosphatidylcholines, sphingomyelins, phosphatidylserines, phosphatidylinositols and phosphoethanolamines to be detected via MALDI(±)-MS in both the positive and negative ion modes. An optimal MALDI-MS protocol for lipidomic monitoring of a single intact embryo is therefore reported with potential applications in human and animal reproduction, cell development and stem cell research.

Proteome regulation during Olea europaea fruit development

BACKGROUND

Widespread in the Mediterranean basin, Olea europaea trees are gaining worldwide popularity for the nutritional and cancer-protective properties of the oil, mechanically extracted from ripe fruits. Fruit development is a physiological process with remarkable impact on the modulation of the biosynthesis of compounds affecting the quality of the drupes as well as the final composition of the olive oil. Proteomics offers the possibility to dig deeper into the major changes during fruit development, including the important phase of ripening, and to classify temporal patterns of protein accumulation occurring during these complex physiological processes.

METHODOLOGY/PRINCIPAL FINDINGS

In this work, we started monitoring the proteome variations associated with olive fruit development by using comparative proteomics coupled to mass spectrometry. Proteins extracted from drupes at three different developmental stages were separated on 2-DE and subjected to image analysis. 247 protein spots were revealed as differentially accumulated. Proteins were identified from a total of 121 spots and discussed in relation to olive drupe metabolic changes occurring during fruit development. In order to evaluate if changes observed at the protein level were consistent with changes of mRNAs, proteomic data produced in the present work were compared with transcriptomic data elaborated during previous studies.

CONCLUSIONS/SIGNIFICANCE

This study identifies a number of proteins responsible for quality traits of cv. Coratina, with particular regard to proteins associated to the metabolism of fatty acids, phenolic and aroma compounds. Proteins involved in fruit photosynthesis have been also identified and their pivotal contribution in oleogenesis has been discussed. To date, this study represents the first characterization of the olive fruit proteome during development, providing new insights into fruit metabolism and oil accumulation process.

Damage of hair follicle stem cells and alteration of keratin expression in external radiation-induced acute alopecia

Alopecia is known as a symptom of acute radiation, yet little is known concerning the mechanism of this phenomenon and the alteration of hair protein profiles. To examine this, 6-week-old male C57/BL6 mice were exposed to 6 Gy of X-ray irradiation, which caused acute alopecia. Their hair and skin were collected, and hair proteins were analyzed with liquid chromatography/electrospray-ionization mass spectrometry and immunohistochemistry. No change was observed in the composition of major hair keratins, such as Krt81, Krt83 and Krt86. However, cytokeratin Krt15 and CD34, which are known as hair follicle stem cell markers, were decreased in alopecic mice. Cytokeratin Krt5, which is known as a marker for basal and undifferentiated keratinocytes, was increased in the epidermis of alopecic mice. These findings suggest that radiation damages hair stem cells and the differentiation of keratinocytes in the epidermis. For the evaluation of radiation exposure, chromosomal aberration is considered to be the gold standard, yet our results suggest that Krt5 may be a novel biological marker for acute radiation symptoms.

Fragmentation reactions of b(5) and a (5) ions containing proline--the structures of a(5) ions

A detailed study has been made of the b(5) and a(5) ions derived from the amides H-Ala-Ala-Ala-Ala-Pro-NH(2), H-Ala-Ala-Ala-Pro-Ala-NH(2), and H-Ala-Ala-Pro-Ala-Ala-NH(2). From quasi-MS(3) experiments it is shown that the product ion mass spectra of the three b(5) ions are essentially identical, indicating macrocyclization/reopening to produce a common mixture of intermediates prior to fragmentation. This is in agreement with numerous recent studies of sequence scrambling in b ions. By contrast, the product ion mass spectra for the a(5) ions show substantial differences, indicating significant differences in the mixture of structures undergoing fragmentation for these three species. The results are interpreted in terms of a mixture of classical substituted iminium ions as well as protonated C-terminal amides formed by cyclization/rearrangement as reported recently for a(4) ions (Bythell, Maître , Paizs, J . Am. Chem. Soc. 2010, 132, 14761-14779). Novel fragment ions observed upon fragmentation of the a(5) ions are protonated H-Pro-NH(2) and H-Pro-Ala-NH(2) which arise by fragmentation of the amides. The observation of these products provides strong experimental evidence for the cyclization/rearrangement reaction to form amides and shows that it also applies to a(5) ions.

Pathways for water loss from doubly protonated peptides containing serine or threonine

The doubly-protonated peptides Ala-Ala-Xaa-Ala-Ala-Ala-Arg show extensive loss of H(2)O when Xaa = Ser or Thr. Using quasi-MS(3) techniques the fragmentation reactions of the [M + 2H - H(2)O](+2) ions have been studied in detail. For both Ser and Thr, the [M + 2H - H(2)O](+2) ions show three primary fragmentation reactions, elimination of CH(3)CH=NH, elimination of one Ala residue, and elimination of two Ala residues, in all cases forming doubly-charged products. From a study of the further fragmentation of these products, it is concluded that elimination of two Ala residues results in formation of a three-membered aziridine ring by interaction with the adjacent amide function as H(2)O is lost. The elimination of one Ala residue results in formation of a five-membered oxazoline ring through interaction with the N-terminal adjacent carbonyl function as H(2)O is lost. The elimination of CH(3)CH=NH appears to involve formation of an eight-membered ring by interaction with the remote N-terminal carbonyl function as H(2)O is lost. However, this initial structure undergoes rearrangement through interaction with the adjacent C-terminal carbonyl function prior to further fragmentation. The [MH - H(2)O](+) ion of Ala-Ala-Ser-Ala-Ala-Ala also shows elimination of CH(3)CH=NH, one Ala residue and two Ala residues.

Effect of the identity of Xaa on the fragmentation modes of doubly-protonated Ala-Ala-Xaa-Ala-Ala-Ala-Arg

The product ion mass spectra resulting from collisional activation of doubly-protonated tryptic-type peptides Ala-Ala-Xaa-Ala-Ala-Ala-Arg have been determined for Xaa = Ala(A), Ser(S), Val(V), Thr(T), Ile(I), Phe(F), Tyr(Y), Sar, Met(M), Trp(W), Pro(P), and Gln(Q). The major fragmentation reaction involves cleavage of the second amide bond (counting from the N-terminus) except for Xaa = Ser and Thr where elimination of H(2)O from the [M + 2H](+2) ion forms the base peak. In general, the extent of cleavage of the second amide bond shows little dependence on the identity of Xaa and little dependence on whether the bond cleavage involves symmetrical bond cleavage to form a y(5)/b(2) ion pair or asymmetrically to form y (5) (+2) and a neutral b(2) species. Notable exceptions to this generalization occur for Xaa equal to Pro or Sar. For Xaa = Pro only cleavage of the second amide bond is observed, consistent with a pronounced proline effect, i.e., cleavage N-terminal to Pro. When Xaa = Sar considerably enhanced cleavage of the second amide bond also is observed, suggesting that at least part of the proline effect relates to the tertiary nature of the amide nitrogen. In the competition between symmetric and asymmetric bond cleavage an attempt to establish a linear free energy correlation in relating ln(y(5)(+2)/y(5)) to PA(H-Xaa-OH) did not lead to a reasonable correlation although the trend of increasing y(5)(+2)/y(5) ratio with increasing proton affinity of H-Xaa-OH was clear. Proline showed a unique behavior in giving a much higher y(5)(+2)/y(5) ratio than any of the other residues studied.

Effect of the His residue on the cyclization of b ions

The MS(n) spectra of the [M + H](+) and b(5) peaks derived from the peptides HAAAAA, AHAAAA, AAHAAA, AAAHAA, and AAAAHA have been measured, as have the spectra of the b(4) ions derived from the first four peptides. The MS(2) spectra of the [M + H](+) ions show a substantial series of b(n) ions with enhanced cleavage at the amide bond C-terminal to His and substantial cleavage at the amide bond N-terminal to His (when there are at least two residues N-terminal to the His residue). There is compelling experimental and theoretical evidence for formation of nondirect sequence ions via cyclization/reopening chemistry in the CID spectra of the b ions when the His residue is near the C-terminus. The experimental evidence is less clear for ions when the His residue is near the N-terminus, although this may be due to the use of multiple alanine residues in the peptide making identifying scrambled peaks more difficult. The product ion mass spectra of the b(4) and b(5) ions from these isomeric peptides with cyclically permuted amino acid sequences are similar, but also show clear differences. This indicates less active cyclization/reopening followed by fragmentation of common structures for b(n) ions containing His than for sequences of solely aliphatic residues. Despite more energetically favorable cyclization barriers for the b(5) structures, the b(4) ions experimental data show more clear evidence of cyclization and sequence scrambling before fragmentation. For both b(4) and b(5) the energetically most favored structure is a macrocyclic isomer protonated at the His side chain.

Proteomics of trypanosomatids of human medical importance

Leishmania spp., Trypanosoma cruzi, and Trypanosoma brucei are protozoan parasites that cause a spectrum of fatal human diseases around the world. Recent completion of the genomic sequencing of these parasites has enormous relevance to the study of their biology and the pathogenesis of the diseases they cause because it opens the door to high-throughput proteomic technologies. This review encompasses studies using diverse proteomic approaches with these organisms to describe and catalogue global protein profiles, reveal changes in protein expression during development, elucidate the subcellular localisation of gene products, and evaluate host-parasite interactions.

Cyclization of peptide b9 ions

The product ion mass spectra obtained by CID of the b(9) ions derived by loss of neutral alanine from the MH+ ion of the peptides Tyr(Ala)9, (Ala)4Tyr(Ala)5, and (Ala)8TyrAla are essentially identical, indicative of full cyclization reaction to a common intermediate before fragmentation. This leads to abundant nondirect sequence ions in the product ion mass spectra of the b9 ions. The product ion mass spectra of the b8 ions from the first two peptides also are essentially identical. The fragmentation of the MH+ ions also leads to low intensity nondirect sequence ions in the product ion mass spectra. N-terminal acetylation blocks the cyclization and eliminates nondirect sequence fragment ions in the product ion mass spectra.

Charge-separation reactions of doubly-protonated peptides: effect of peptide chain length

The collision induced dissociation of doubly-protonated (Ala)(x)His (x = 5, 6, 7, 8, 10) peptides have been studied. The major fragmentation reactions observed are symmetrical amide bond cleavages to give the complementary b(m) and y(N-m) ions, where N is the total number of residues in the peptide. Minor asymmetric cleavage to give doubly-protonated y ions also is observed, involving cleavage near the N-terminus. The shorter peptides (x = 5, 6, 7) show major cleavage of the second amide bond to yield b2 and y(N-2) ions, while (Ala)10His shows major symmetrical cleavage at the fourth and fifth amide bonds. (Ala)8His appears to be a transitional peptide in showing substantial symmetrical cleavage at the second, fourth, and fifth amide bonds. The results are in general agreement with the bifurcating nature of charge separation noted by Zubarev (J. Am. Soc. Mass Spectrom.2008, 19, 1755-1763) from a statistical analysis of a large body of doubly-protonated tryptic peptide CID mass spectra. It is shown that the b2 ion derived from doubly-protonated (Ala)5His has a protonated oxazolone structure.

Recent advances in capillary and microfluidic platforms with MS detection for the analysis of phosphoproteins

Reversible protein phosphorylation represents a key regulatory mechanism that triggers essential cellular signaling events. The large-scale characterization of protein phosphorylation in a cell represents, therefore, the objective of many biological studies that aim at elucidating the complex signaling pathways that are involved in the progression and/or regression of a disease. The recent implementation of novel MS detection strategies has significantly advanced the capabilities for interrogating the complex cellular phosphoproteome. Simultaneously, the current advent of miniaturized technologies has clearly demonstrated the superior performance of microfluidic instrumentation for bioanalytical and biological applications that cope with speed, sensitivity and throughput-related demands. This review aims at providing an update on the latest developments regarding the interfacing of microfluidic devices with MS detection for exploring the challenging area of phosphoproteomics.

Microfluidics with MALDI analysis for proteomics--a review

Various microfluidic devices have been developed for proteomic analyses and many of these have been designed specifically for mass spectrometry detection. In this review, we present an overview of chip fabrication, microfluidic components, and the interfacing of these devices to matrix-assisted laser desorption ionization (MALDI) mass spectrometry. These devices can be directly coupled to the mass spectrometer for on-line analysis in real-time, or samples can be analyzed on-chip or deposited onto targets for off-line readout. Several approaches for combining microfluidic devices with analytical functions such as sample cleanup, digestion, and separations with MALDI mass spectrometry are discussed.

Peptide sequence scrambling through cyclization of b(5) ions

The CID mass spectra of the MH(+) ions and the b(5) ions derived therefrom have been determined for the hexapeptides YAAAAA, AYAAAA, AAYAAA, AAAYAA, and AAAAYA. The CID mass spectra for the b(5) ions derived from the five isomers are essentially identical and show abundant ion signals for nonsequence b ions. This result is consistent with cyclization of the b(5) ions to a cyclic pentapeptide before fragmentation; this cyclic peptide can open at various positions, leading to losses of amino acid residues that are not characteristic of the original amino acid sequence. These nonsequence b ions are also observed in the fragmentation of the MH(+) ions and increase substantially in importance with increasing collision energy. A comparison of the fragmentation of AAAYAA and Ac-AAAYAA indicates that N-acetylation eliminates the cyclization of b(5) ions and, thus, eliminates the nonsequence ions in the CID mass spectra of both b(5) and MH(+) ions.

Inhibiting matrix metalloproteinase-2 reduces protein release into coronary effluent from isolated rat hearts during ischemia-reperfusion

BACKGROUND

Previous studies have shown that the disruption of the coronary endothelium and the increase in its permeability during ischemia-reperfusion (I/R), are linked to matrix metalloproteinase-2 (MMP-2) activity. Studies from our group have shown that during I/R, activity of MMP-2 in the coronary effluent increases and this increase is associated with cardiac dysfunction, which in turn, can be prevented by MMP inhibitors. Therefore, we hypothesize that inhibiting MMPs reduces the MMP-2 dependent disruption of the coronary endothelium and subsequent protein release during I/R.

METHODS

Isolated rat hearts were perfused in the Langendorff mode at a constant pressure and subjected to 15, 20 or 30 min no-flow ischemia followed by 30 min of reperfusion. The MMP inhibitors, o-phenanthroline (Phen, 100 microM) or doxycycline (Doxy, 30 microM) an inhibitors of MMPs, were added to the perfusion solution 10 min before ischemia and for the first 10 min of reperfusion. The coronary effluents were collected during perfusion for protein analysis. Creatine kinase was measured as an index of cellular damage. Endothelial integrity was assessed by measuring coronary flow and by measuring the levels of serotransferrin and interstitial albumin in the coronary effluent. Additionally, damage to the endothelium was assessed histologically by light microscopy analysis of the cellular structure of the myocardium. MMP-2 activity was measured by zymography in hearts subjected to 15, 20 and 30 min of ischemia without reperfusion.

RESULTS

MMP-2 activity was increased in heart tissue at the end of ischemia and was correlated with duration of ischemia. The post-ischemia decrease in coronary flow, and the increase in the release of serotransferrin and albumin were attenuated by Phen. Edema (another indirect marker of endothelial damage) was observed in I/R heart and the edema was abolished in I/R heart treated with MMP inhibitors.

CONCLUSION

MMP inhibition not only reduces cardiac mechanical dysfunction but also reduces endothelial damage resulting from cardiac I/R injury.

Detecting the site of phosphorylation in phosphopeptides without loss of phosphate group using MALDI TOF mass spectrometry

Phosphopeptides with one and four phosphate groups were characterized by MALDI mass spectrometry. The molecular ion of monophosphopeptide could be detected both as positive and negative ions by MALDI TOF with delayed extraction (DE) and in the reflector mode. The tetraphospho peptide could be detected in linear mode. When MS/MS spectra of the monophospho peptides were obtained in a MALDI TOF TOF instrument by CID, b and y ions with the intact phosphate group were observed, in addition the b and y ions without the phosphate group. Our study indicates that it is possible to detect phosphorylated peptides with out the loss of phosphate group by MALDI TOF as well as MALDI TOF TOF instruments with delayed extraction and in the reflector mode.

Application of two-dimensional electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for proteomic analysis of the sexually transmitted parasite Trichomonas vaginalis

Trichomonas vaginalis is a sexually transmitted protozoan parasite that infects the human urogenital tract causing trichomoniasis, a worldwide disease. In this work, a fresh clinical isolate of T. vaginalis was used for study of the protein expression in this species. Two-dimensional gel electrophoresis (2-DE) and MALDI-TOF/TOF mass spectrometry (MS) were employed to create a reference map of soluble proteins in the pH range 4-7. A set of 116 proteins belonging to functional classes expressed in high and low abundance was identified by peptide mass fingerprinting and tandem MS. These identifications corresponded to 67 different proteins, suggesting that post-translational modifications are common phenomena in T. vaginalis. Identified proteins were classified into 16 groups according to biological processes. Among detected proteins we identified the major enzymes involved in both cytosolic and hydrogenosomal metabolic pathways, as well as putative protein targets for new drug design. In addition, this analysis allows validation of previous gene predictions confirming the expression of 15 hypothetical proteins. Finally, the findings here reported represent the first reference proteome map of T. vaginalis and the first steps towards the description of a comprehensive proteome map of this parasite.

Fragmentation of protonated dipeptides containing arginine. Effect of activation method

The fragmentation reactions of the protonated dipeptides Gly-Arg and Arg-Gly have been studied using collision-induced dissociation (CID) in a quadrupole ion trap, by in-source CID in a single-quadrupole mass spectrometer and by CID in the quadrupole cell of a QqTOF mass spectrometer. In agreement with earlier quadrupole ion trap studies (Farrugia, J. M.; O'Hair, R. A. J., Int. J. Mass Spectrom., 2003, 222, 229), the CID mass spectra obtained with the ion trap for the MH(+) ions and major fragment ions are very similar for the two isomers indicating rearrangement to a common structure before fragmentation. In contrast, in-source CID of the MH(+) ions and QqTOF CID of the MH(+), [MH - NH(3)](+) and [MH <23 HN = C(NH(2))(2)](+) ions provide distinctly different spectra for the isomeric dipeptides, indicating that rearrangement to a common structure has not occurred to a significant extent under these conditions even near the threshold for fragmentation in the QqTOF instrument. Clearly, under normal operating conditions significantly different fragmentation behavior is observed in the ion trap and beam-type experiments. This different behavior probably can be attributed to the shorter observation times and concomitant higher excitation energies in the in-source and QqTOF experiments compared to the long observation times and lower excitation energies relevant to the ion trap experiments. Based largely on elemental compositions derived from accurate mass measurements in QqTOF studies fragmentation schemes are proposed for the MH(+), [MH - NH(3)](+), and [MH - (HN = C(NH(2))(2))](+) ions.

Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry

Proteins from biological samples are often identified by mass spectrometry (MS) with the two following "bottom-up" approaches: peptide mass fingerprinting or peptide sequence tag. Nevertheless, these strategies are time-consuming (digestion, liquid chromatography step, desalting step), the N- (or C-) terminal information often lacks and post-translational modifications (PTMs) are hardly observed. The in-source decay (ISD) occurring in a matrix assisted laser desorption/ionization (MALDI) source appears an interesting analytical tool to obtain N-terminal sequence, to identify proteins and to characterize PTMs by a "top-down" strategy. The goal of this review deals with the usefulness of the ISD technique in MALDI source in proteomics fields. In the first part, the ISD principle is explained and in the second part, the use of ISD in proteomic studies is discussed for protein identification and sequence characterization.

Chronic cyclophosphamide exposure alters the profile of rat sperm nuclear matrix proteins

Chronic exposure of male rats to the alkylating agent cyclophosphamide, a well-known male-mediated developmental toxicant, alters gene expression in male germ cells as well as in early preimplantation embryos sired by cyclophosphamide-exposed males. Sperm DNA is organized by the nuclear matrix into loop-domains in a sequence-specific manner. In somatic cells, loop-domain organization is involved in gene regulation. Various structural and functional components of the nuclear matrix are targets for chemotherapeutic agents. Consequently, we hypothesized that cyclophosphamide treatment would alter the expression of sperm nuclear matrix proteins. Adult male rats were treated for 4 wk with saline or cyclophosphamide (6.0 mg kg(-1) day(-1)), and the nuclear matrix was extracted from cauda epididymal sperm. Proteins were analyzed by two-dimensional gel electrophoresis. Identified proteins within the nuclear matrix proteome were mainly involved in cell structure, transcription, translation, DNA binding, protein processing, signal transduction, metabolism, cell defense, or detoxification. Interestingly, cyclophosphamide selectively induced numerous changes in cell defense and detoxification proteins, most notably, in all known forms of the antioxidant enzyme glutathione peroxidase 4, in addition to an uncharacterized 54-kDa form; an overall increase in glutathione peroxidase 4 immunoreactivity was observed in the nuclear matrix extracts from cyclophosphamide-exposed spermatozoa. An increase in glutathione peroxidase 4 expression suggests a role for this enzyme in maintaining nuclear matrix stability and function. These results led us to propose that a change in composition of the nuclear matrix in response to drug exposure was a factor in altered sperm function and embryo development.

Prolactin-induced changes in protein expression in human pancreatic islets

Ex vivo islet cell culture prior to transplantation appears as an attractive alternative for treatment of type 1 diabetes. Previous results from our laboratory have demonstrated beneficial effects of human prolactin (rhPRL) treatment on human islet primary cultures. In order to probe into the molecular events involved in the intracellular action of rhPRL in these cells, we set out to identify proteins with altered expression levels upon rhPRL cell treatment, using two-dimensional (2D) gel electrophoresis and mass spectrometry (MS). An average of 300 different protein spots were detected, 14 of which were modified upon rhPRL treatment (p<0.01), of which 12 were successfully identified using MS and grouped according to their biological functions. In conclusion, our study provides, for the first time, information about proteins that could be critically involved in PRL's action on human pancreatic islets, and facilitate identification of new and specific targets involved in islet cell function and proliferation.

A novel high-capacity ion trap-quadrupole tandem mass spectrometer

We describe a prototype tandem mass spectrometer that is designed to increase the efficiency of linked-scan analyses by >100-fold over conventional linked-scan instruments. The key element of the mass spectrometer is a novel high ion capacity ion trap, combined in tandem configuration with a quadrupole collision cell and a quadrupole mass analyzer (i.e. a TrapqQ configuration). This ion trap can store >10(6) ions without significant degradation of its performance. The current mass resolution of the trap is 100-450 full width at half maximum for ions in the range 800-4000 m/z, yielding a 10-20 m/z selection window for ions ejected at any given time into the collision cell. The sensitivity of the mass spectrometer for detecting peptides is in the low femtomole range. We can envisage relatively straightforward modifications to the instrument that should improve both its resolution and sensitivity. We tested the tandem mass spectrometer for collecting precursor ion spectra of all the ions stored in the trap and demonstrated that we can selectively detect a phosphopeptide in a mixture of non-phosphorylated peptides. Based on this prototype instrument, we plan to construct a fully functional model of the mass spectrometer for detecting modification sites on proteins and profiling their abundances with high speed and sensitivity.

Genistein-induced proteome changes in the human endometrial carcinoma cell line, ishikawa

Epidemiological studies have shown that Asian populations display a lower incidence of hormone-dependant cancers, cardiovascular disease, osteoporosis, and menopausal ailments compared to Western societies. Available data support the proposal that lower incidence is associated with the high dietary consumption of isoflavones, such as genistein. This study used two-dimensional electrophoresis to characterize the effect of genistein on the proteome of an endometrial tumor cell model, namely the Ishikawa cell line. Proteome maps displaying approx 1800 proteins were obtained from cells treated with vehicle or genistein at physiologically attainable concentrations of 0.5, 5, or 50 μM or supra-physiological concentration, 500 μM. The effects of genistein on protein expression were characterized using image analysis software. A total 65 protein spots displayed a significant decrease in expression and 32 proteins displayed a significant increase in expression. Of these protein spots, 29 were randomly selected for characterization by matrix assisted laser desorption/ionization tandem mass spectrometry, yielding 18 different proteins. This type of analysis enabled the characterization of a wide range of cellular proteins and allowed for the identification of functional and biochemical pathways that may be regulated or affected by genistein, including cellular transcription, cell proliferation, stress response, or modulation of oncogenic pathways.

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

Cloning and sequencing of the Bet v 1-homologous allergen Fra a 1 in strawberry (Fragaria ananassa) shows the presence of an intron and little variability in amino acid sequence

The Fra a 1 allergen in strawberry (Fragaria ananassa) is homologous to the major birch pollen allergen Bet v 1, which has numerous isoforms differing in terms of amino acid sequence and immunological impact. To map the extent of sequence differences in the Fra a 1 allergen, PCR cloning and sequencing was applied. Several genomic sequences of Fra a 1, with a length of either 584, 591 or 594 nucleotides, were obtained from three different strawberry varieties. All contained one intron, with the length of either 101 or 110 nucleotides. By sequencing 30 different clones, eight different DNA sequences were obtained, giving in total five potential Fra a 1 protein isoforms, with high sequence similarity (>97% sequence identity) and only seven positions of amino acid variability, which were largely confirmed by mass spectrometry of expressed proteins. We conclude that the sequence variability in the strawberry allergen Fra a 1 is small, within and between strawberry varieties, and that multiple spots, previously detected in 2DE, are presumably due to differences in post-translational modification rather than differences in amino acid sequence. The most abundant Fra a 1 isoform sequence, recombinantly expressed in Escherichia coli after removal of the intron, was recognized by IgE from strawberry allergic patients. It cross-reacted with antibodies to Bet v 1 and the homologous apple allergen Mal d 1 (61 and 78% sequence identity, respectively), and will be used in further analyses of variation in Fra a 1-expression.

Comparison of different separation technologies for proteome analyses: Isoform resolution as a prerequisite for the definition of protein biomarkers on the level of posttranslational modifications

In this article we evaluate methods used to reveal the molecular complexity, which is generated in biological samples by posttranslational modifications (PTM) of proteins. We show how distinct molecular differences on the level of phosphorylation sites in a single protein (ovalbumin) can be resolved with different success using 1D and 2D gel-electrophoresis and reversed-phase liquid chromatography (LC) with monolithic polystyrol-divinylbenzol (PS-DVB) columns for protein separation, and matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) for protein identification. Phosphorylation site analysis was performed using enzymatic dephosphorylation in combination with differential peptide mass mapping. Liquid chromatography-MALDI-TOF MS coupling with subsequent on-target tryptic protein digestion turned out to be the fastest method tested but yielded low resolution for the analysis of PTM, whereas 2D gel-electrophoresis, due to its unique capability of resolving highly complex isoform pattern, turned out to be the most suitable method for this purpose. The evaluated methods complement one another and in connection with efficient technologies for differential and quantitative analysis, these approaches have the potential to reveal novel molecular details of protein biomarkers.

Proteomics of the human brain: sub-proteomes might hold the key to handle brain complexity

Proteomics is a promising approach, which provides information about the expression of proteins and increasingly finds application in life science and disease research. Meanwhile, proteomics has proven to be applicable even on post mortem human brain tissue and has opened a new area in neuroproteomics. Thereby, neuroproteomics is usually employed to generate large protein profiles of brain tissue, which mostly reflect the expression of highly abundant proteins. As a complementary approach, the focus on sub-proteomes would enhance more specific insight into brain function. Sub-proteomes are accessible via several strategies, including affinity pull-down approaches, immunoprecipitation or subcellular fractionation. The extraordinary potential of subcellular proteomics to reveal even minute differences in the protein constitution of related cellular organelles is exemplified by a recent global description of neuromelanin granules from the human brain, which could be identified as pigmented lysosome-related organelles.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update covering the period 1999-2000

This review describes the use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates and continues coverage of the field from the previous review published in 1999 (D. J. Harvey, Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates, 1999, Mass Spectrom Rev, 18:349-451) for the period 1999-2000. As MALDI mass spectrometry is acquiring the status of a mature technique in this field, there has been a greater emphasis on applications rather than to method development as opposed to the previous review. The present review covers applications to plant-derived carbohydrates, N- and O-linked glycans from glycoproteins, glycated proteins, mucins, glycosaminoglycans, bacterial glycolipids, glycosphingolipids, glycoglycerolipids and related compounds, and glycosides. Applications of MALDI mass spectrometry to the study of enzymes acting on carbohydrates (glycosyltransferases and glycosidases) and to the synthesis of carbohydrates, are also covered.

Detection of phosphorylated peptides in proteomic analyses using microfluidic compact disk technology

A compact disk (CD)-based microfluidic method for selective detection of phosphopeptides by mass spectrometry is described. It combines immobilized metal affinity chromatography (IMAC) and enzymatic dephosphorylation. Phosphoproteins are digested with trypsin and processed on the CD using nanoliter scale IMAC with and without subsequent in situ alkaline phosphatase treatment. This is followed by on-CD matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Dephosphorylation of the IMAC-enriched peptides allows selective phosphopeptide detection based on the differential mass maps generated (mass shifts of 80 Da or multiples of 80 Da). The CD contains 96 microstructures, each with a 16 nL IMAC microfluidic column. Movement of liquid is controlled by differential spinning of the disk. Up to 48 samples are distributed onto the CD in two equal sets. One set is for phosphopeptide enrichment only, the other for identical phosphopeptide enrichment but combined with in situ dephosphorylation. Peptides are eluted from the columns directly into MALDI target areas, still on the CD, using a solvent containing the MALDI matrix. After crystallization, the CD is inserted into a MALDI mass spectrometer for analysis down to the femtomole level. The average success rate in phosphopeptide detection is over 90%. Applied to noncharacterized samples, the method identified two novel phosphorylation sites, Thr 735 and Ser 737, in the ligand-binding domain of the human mineralocorticoid receptor.

Mass spectrometric approaches for characterizing bacterial proteomes

The emergence of advanced liquid chromatography mass spectrometry technologies for characterizing very complex mixtures of proteins has greatly propelled the field of proteomics, the goal of which is the simultaneous examination of all the proteins expressed by an organism. This research area represents a paradigm shift in molecular biology by attempting to provide a top-down qualitative and quantitative view of all the proteins (including their modifications and interactions) that are essential for an organism's life cycle, rather than targeting a particular protein family. This level of global protein information about an organism such as a bacterium can be combined with genomic and metabolomic data to enable a systems biology approach for understanding how these organisms live and function.