A mechanism of melanogenesis mediated by E-cadherin downregulation and its involvement in solar lentigines.

OBJECTIVE: Intensive studies have revealed that pleiotropic melanocytic factors are associated with age-spot formation. Dysfunctional keratinocyte differentiation is thought to be an upstream cause of age-spot formation. Although it has been shown that keratinocyte differentiation is mediated by the cell-cell contact factor E-cadherin, its involvement in age-spot formation remains unknown. Thus, to determine the origin of age-spots and an integrated solution for the same, we focused on E-cadherin expression in the present study. METHODS: First, we assessed the solar lentigines in cutaneous and cultured cells by means of immunofluorescence staining. Following that, keratinocytes treated with siRNAs against E-cadherin were co-cultured with melanocytes, and the secreted factors were identified by means of proteomic analysis of the culture supernatants. We also performed quantitative PCR to assess melanogenesis activity and screen ingredients. For behavioural analysis of melanocytes, we performed time-lapse imaging using confocal laser scanning microscopy. RESULTS: E-cadherin expression was downregulated in the epidermis of the solar lentigines, suggesting its involvement in age-spot formation. E-cadherin knocked down keratinocytes not only promoted the secretion of melanocytic/inflammatory factors but also increased melanogenesis by upregulating the expression of melanogenesis factors. Furthermore, live-imaging showed that the downregulation of E-cadherin inhibited melanocyte dynamics and accelerated melanin uptake. Finally, we identified Rosa multiflora fruit extract as a solution that can upregulate E-cadherin expression in keratinocytes. CONCLUSION: Our findings showed that E-cadherin downregulation triggers various downstream melanocytic processes, such as the secretion of melanocytic factors and melanogenesis. Additionally, we showed that the Rosa multiflora fruit extract upregulated E-cadherin expression in keratinocytes.

OBJECTIF: Des études intensives ont révélé que les facteurs mélanocytaires pléiotropiques sont associés à la formation de taches de vieillesse. On pense que la différenciation des kératinocytes dysfonctionnels est une cause en amont de la formation des taches de vieillesse. Bien qu'il ait été démontré que la différenciation des kératinocytes est médiée par le facteur de contact cellule-cellule E-cadhérine, son implication dans la formation des taches de vieillesse reste inconnue. Ainsi, pour déterminer l'origine des taches de vieillesse et une solution intégrée pour celles-ci, nous nous sommes concentrés sur l'expression de la E-cadhérine dans la présente étude. MÉTHODES: Tout d'abord, nous avons évalué les lentigines solaires dans les cellules cutanées et cultivées au moyen d'une coloration par immunofluorescence. Par la suite, les kératinocytes traités avec des siRNA contre l'E-cadhérine ont été co-cultivés avec des mélanocytes, et les facteurs sécrétés ont été identifiés au moyen d'une analyse protéomique des surnageants de culture. Nous avons également effectué une PCR quantitative pour évaluer l'activité de la mélanogénèse et dépister les ingrédients. Pour l'analyse comportementale des mélanocytes, nous avons réalisé une imagerie accélérée à l'aide de la microscopie confocale à balayage laser. RÉSULTATS: L'expression de l'E-cadhérine a été régulée à la baisse dans l'épiderme des lentigines solaires, suggérant son implication dans la formation des taches de vieillesse. Les kératinocytes dans lesquels l'E-cadhérine a été réduite non seulement ont favorisé la sécrétion de facteurs mélanocytaires/inflammatoires, mais ont également accru la mélanogenèse en régulant à la hausse l'expression de facteurs de mélanogenèse. De plus, l'imagerie en direct a montré que la régulation négative de l'E-cadhérine inhibait la dynamique des mélanocytes et accélérait l'absorption de la mélanine. Enfin, nous avons identifié l'extrait de fruit de Rosa multiflora comme une solution capable de réguler positivement l'expression de l'E-cadhérine dans les kératinocytes. CONCLUSION: Nos résultats ont montré que la régulation négative de la E-cadhérine déclenche divers processus mélanocytaires en aval, tels que la sécrétion de facteurs mélanocytaires et la mélanogénèse. De plus, nous avons montré que l'extrait de fruit de Rosa multiflora régulait à la hausse l'expression de l'E-cadhérine dans les kératinocytes.

Oral Supplementation of Collagen Peptides Improves Skin Hydration by Increasing the Natural Moisturizing Factor Content in the Stratum Corneum: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial.

INTRODUCTION: We aimed to investigate the effect of orally ingested collagen peptides (CPs) on skin condition and elucidate their mechanism of action. METHODS: A randomized, placebo-controlled, double-blind trial was conducted in 99 healthy Japanese women, aged 35-50 years. The subjects were randomized into 3 groups (33 subjects/group) to receive 1 or 5 g of CP or placebo once daily for 12 weeks. Skin water content, transepidermal water loss (TEWL), skin elasticity, and skin thickness were evaluated before treatment and after 4, 8, and 12 weeks of treatment. The level of natural moisturizing factor (NMF) constituents in the stratum corneum (SC) was quantified before treatment and after 12 weeks of treatment. RESULTS: Oral ingestion of CP increased the water content in the SC and epidermis and decreased TEWL. Furthermore, the NMF level in the SC was increased. However, skin elasticity and skin thickness remained unchanged. CONCLUSIONS: The improvement in skin water content following the oral ingestion of CP can be attributed to an increase in the level of NMF in the SC. TRIAL REGISTRATION: UMIN000030375 (retrospectively registered).

Influence of hydrophilic additives on the signal intensity in electrospray ionization of flavonoid glycosides.

RATIONALE: The influence of hydrophilic additives glycine, glucose, and glycerol on electrospray ionization (ESI) signal intensity of flavonoid glycosides and a nonreducing disaccharide is examined. The addition of excess glycine to the ESI solution would affect signal intensity more than glucose and glycerol due to its strong hydration capability. METHODS: The ESI signal response upon the addition of excess additives prepared was estimated in both selected ion monitoring and scan mode. All the mass spectrometry data were acquired in negative ion mode, because negative ion mode is recommended for saccharide compounds. RESULTS: The addition of glycine to the ESI solution of flavonoid glycosides and trehalose enhanced signal intensity, whereas the addition of glucose and glycerol had little effect. The signal intensity of rutin was higher than that of naringin and hesperidin, in accordance with their solubility in ESI solution. Trehalose molecules specifically interacted with glycine molecules to form a 1:1 trehalose-glycine complex, whereas the flavonoid glycosides did not produce such complex ions. CONCLUSIONS: The ESI signal enhancement of the saccharides with the additive glycine can be explained by its strong hydration capability, with the deprotonated carboxylic oxygens of zwitterionic glycine molecules strongly interacting with water hydrogen atoms resulting in strong hydration enthalpy. Consequently, glycine molecules set the analytes free from solvation with water molecules in the ESI droplets.

Influence of Solvent Composition and Surface Tension on the Signal Intensity of Amino Acids in Electrospray Ionization Mass Spectrometry.

The influence of solvent composition and surface tension on the signal intensity of deprotonated molecules [M-H]- in electrospray ionization mass spectrometry (ESI MS) was evaluated using alanine (Ala), threonine (Thr) and phenylalanine (Phe), which have differing levels of hydrophobicity. The surface tension of the ESI solution was varied by changing the ratio of the organic solvents methanol (MeOH) and acetonitrile (MeCN) in water (H2O). In ESI MS, the signal intensity of all the amino acids was increased with decreasing surface tension for the two solutions, H2O/MeOH and H2O/MeCN. The use of H2O/MeCN was more favorable for achieving a strong signal for the analytes compared to H2O/MeOH. The smaller vaporization enthalpy of MeCN compared to MeOH was proposed as one of the most plausible explanation for this. The order of the signal intensity of amino acids was Phe>Thr>Ala, the same order as their hydrophobicity. It can be practically concluded that the use of solutions with lower surface tensions and lower vaporization enthalpies would result in higher signal intensities in ESI MS.

Key component of inflammasome, NLRC4, was identified in the lesional epidermis of psoriatic patients.

Inflammasomes are multimolecular complexes that control the inflammatory response. The function of inflammasomes in the pathogenesis of psoriasis is still unclear. To clarify the relationship between inflammasomes and the pathophysiology of psoriasis, and in particular, to identify molecules interacting with caspase-1, a crucial component of inflammasomes, scale extracts obtained from patients with psoriasis were immunoprecipitated with anti-caspase-1 antibody and analyzed by liquid chromatography coupled with electrospray tandem mass spectrometry (LC-MS/MS). The expression of the inflammasome component was assessed by immunohistochemical analysis and an in vitro assay. We identified several candidates for caspase-1-interacting proteins from the psoriatic scale extracts by immunoprecipitation and LC-MS/MS. Nucleotide-binding oligomerization domain-containing protein-like receptor family CARD domain-containing protein 4 (NLRC4) was the only inflammasome component among the candidates; thus, the protein is considered to be a key factor of inflammasomes in psoriasis. No inflammasome component was found in the extracts of atopic dermatitis or normal skin by LC-MS/MS. Immunohistochemical analysis demonstrated upregulation of NLRC4 in the lesional epidermis of some psoriatic patients whereas weak expression of NLRC4 was detected in the normal and non-lesional epidermis. The mRNA expression of the NLRC4 gene increased in keratinocytes at confluency, 48 h after air exposure and after the addition of 1.5 mmol/L calcium chloride. Our findings suggest that NLRC4 may be involved in the exacerbation or modification of psoriatic lesions.

Mass Spectrometry in Cosmetic Science: Advanced Ionization Techniques for Detecting Trace Molecules in or on Human Skin.

To provide safe and effective products to customers in the cosmetic industry, mass spectrometry (MS) is an indispensable analytical tool. In addition to its outstanding sensitivity and specificity, the method is applicable to a wide variety of compounds, which makes it irreplaceable for the development of cosmetics, which requires the analysis of complex systems. Because most cosmetic products are applied directly to the skin and function as they are designed, monitoring the molecular compositions of endogenous or exogenous compounds in or on the skin is crucial to ensure the safety and efficacy of a cosmetic product. Recent advancements in MS and ionization techniques, such as MS imaging and ambient ionization, now provide access to richer and deeper molecular information with less time and effort. This brief review discusses advanced ionization techniques that are currently used in the field of cosmetic science using two examples, namely, the use of desorption electrospray ionization and zero-volt paperspray ionization to detect trace molecules in or on human skin.

The corrected structure of depressoside, an antioxidative iridoid glucoside extracted from the flowers of Gentiana urnula Harry Sm.

Three known iridoid glucosides (gentiournoside A, gentiournoside E and depressoside) were isolated from the flowers of Gentiana urnula Harry Sm. through activity-guided fractionations with a 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay. All three compounds exhibited excellent DPPH radical scavenging activities (IC50: 10-20 µmol L(-1)) comparable to that of ascorbic acid and Trolox. However, examination of the NMR data revealed that the reported chemical structure of depressoside, previously isolated from the leaves of G. depressa, needed correcting due to incorrect elucidation around C-7 of the iridane skeleton, and was corrected to 6-ß-(2,3-dihydroxyphenyl)-D-glucosyl 7-O-(2,3-dihydroxybenzoyl)-loganate. Depressoside exhibited a much higher scavenging activity against superoxide radicals (IC50: 45.5 µmol L(-1)) than the other two extracted compounds (IC50: more than 900 µmol L(-1)) due to the crucial presence of a pyrogallyl unit.

Zero volt paper spray ionization mass spectrometry for direct analysis of samples on filter paper substrate.

RATIONALE: Zero volt paper spray ionization (zvPSI) is a newly developed sample introduction/ionization technique for mass spectrometry (MS), which combines favorable features of paper spray ionization (PSI) and solvent-assisted inlet ionization (SAII). With a simple platform similar to PSI, zvPSI allows direct MS analysis of a broad type of samples (liquid, (semi-)solid, and imprint) without applying voltage. METHODS: In zvPSI-MS, a rectangular paper slip was used as a sample loader, extraction medium, and droplet emitter to introduce sample extract into the inlet of a mass spectrometer. For (semi-)solid and imprint samples, analyte(s) was directly extracted with solvent and instantaneously introduced into a mass spectrometer by aspiration. Solution samples were analyzed after being dried-up or by dispensing directly onto paper. Ionization was achieved by SAII and ionized molecules were detected by an ion-trap mass spectrometer. RESULTS: The developed method allowed direct voltage-free MS analysis of samples on filter paper substrate. Favorable features of PSI and SAII were successfully combined, such as fast data acquisition, flexible sample handlings, and direct extraction capability from solid samples (PSI), with no need for external high-voltage, laser, or nebulizing gas to convert analytes into gas-phase ions (SAII). Comparable to PSI and SAII, a wide variety of compounds such as amino acids, peptides, lipids and synthetic polymers were shown to be analyzed. CONCLUSIONS: The developed method (zvPSI-MS) expanded the analytical utility of PSI and SAII to voltage-free direct MS analysis of a broad type of samples (liquid, (semi-)solid, and imprint).

Mesotrypsin and caspase-14 participate in prosaposin processing: potential relevance to epidermal permeability barrier formation.

A proteomics-based search for molecules interacting with caspase-14 identified prosaposin and epidermal mesotrypsin as candidates. Prosaposin is a precursor of four sphingolipid activator proteins (saposins A-D) that are essential for lysosomal hydrolysis of sphingolipids. Thus, we hypothesized that caspase-14 and mesotrypsin participate in processing of prosaposin. Because we identified a saposin A sequence as an interactor with these proteases, we prepared a specific antibody to saposin A and focused on saposin A-related physiological reactions. We found that mesotrypsin generated saposins A-D from prosaposin, and mature caspase-14 contributed to this process by activating mesotrypsinogen to mesotrypsin. Knockdown of these proteases markedly down-regulated saposin A synthesis in skin equivalent models. Saposin A was localized in granular cells, whereas prosaposin was present in the upper layer of human epidermis. The proximity ligation assay confirmed interaction between prosaposin, caspase-14, and mesotrypsin in the granular layer. Oil Red staining showed that the lipid envelope was significantly reduced in the cornified layer of skin from saposin A-deficient mice. Ultrastructural studies revealed severely disorganized cornified layer structure in both prosaposin- and saposin A-deficient mice. Overall, our results indicate that epidermal mesotrypsin and caspase-14 work cooperatively in prosaposin processing. We propose that they thereby contribute to permeability barrier formation in vivo.

Kallikrein-related peptidase 5 functions in proteolytic processing of profilaggrin in cultured human keratinocytes.

Filaggrin protein is synthesized in the stratum granulosum of the skin and contributes to the formation of the human skin barrier. Profilaggrin is cleaved by proteolytic enzymes and converted to functional filaggrin, but its processing mechanism remains not fully elucidated. Kallikrein-related peptidase 5 (KLK5) is a major serine protease found in the skin, which is secreted from lamellar granules following its expression in the stratum granulosum and activated in the extracellular space of the stratum corneum. Here, we searched for profilaggrin-processing protease(s) by partial purification of epidermal extracts and found KLK5 as a possible candidate. We used high performance liquid chromatography coupled with electrospray tandem mass spectrometry to show that KLK5 cleaves profilaggrin. Furthermore, based on a proximity ligation assay, immunohistochemistry, and immunoelectron microscopy analysis, we reveal that KLK5 and profilaggrin co-localize in the stratum granulosum in human epidermis. KLK5 knockdown in normal cultured human epidermal keratinocytes resulted in higher levels of profilaggrin, indicating that KLK5 potentially functions in profilaggrin cleavage.

DOCK7 is a critical regulator of the RAGE-Cdc42 signaling axis that induces formation of dendritic pseudopodia in human cancer cells.

Cellular migration is a fundamental process linked to cancer metastasis. Growing evidence indicates that the receptor for advanced glycation end products (RAGE) plays a pivotal role in this process. With regard to downstream signal transducers of RAGE, diaphanous-1 and activated small guanine nucleotide triphosphatases, Rac1 and Cdc42, have been identified. To obtain precise insight into the direct downstream signaling mechanism of RAGE, we screened for proteins interacting with the cytoplasmic domain of RAGE employing an immunoprecipitation-liquid chromatography coupled with an electrospray tandem mass spectrometry system. In the present study, we found that the cytoplasmic domain of RAGE interacted with an atypical DOCK180-related guanine nucleotide exchange factor, dedicator of cytokinesis protein 7 (DOCK7). DOCK7 bound to the RAGE cytoplasmic domain and transduced a signal to Cdc42, resulting in the formation of abundant highly branched filopodia-like protrusions, dendritic pseudopodia. Blocking of the function of DOCK7 greatly abrogated the formation of dendritic pseudopodia and suppressed cellular migration. These results indicate that DOCK7 functions as an essential and downstream regulator of RAGE-mediated cellular migration through the formation of dendritic pseudopodia.

S100A9 is a novel ligand of EMMPRIN that promotes melanoma metastasis.

The calcium-binding proteins S100A8 and S100A9 can dimerize to form calprotectin, the release of which during tissue damage has been implicated in inflammation and metastasis. However, receptor(s) mediating the physiologic and pathophysiologic effects of this damage-associated "danger signal" are uncertain. In this study, searching for candidate calprotectin receptors by affinity isolation-mass spectrometry, we identified the cell surface glycoprotein EMMPRIN/BASIGIN (CD147/BSG). EMMPRIN specifically bound to S100A9 but not S100A8. Induction of cytokines and matrix metalloproteases (MMP) by S100A9 was markedly downregulated in melanoma cells by attenuation of EMMPRIN. We found that EMMPRIN signaling used the TNF receptor-associated factor TRAF2 distinct from the known S100-binding signaling pathway mediated by RAGE (AGER). S100A9 strongly promoted migration when EMMPRIN was highly expressed, independent of RAGE, whereas EMMPRIN blockade suppressed migration by S100A9. Immunohistologic analysis of melanomas revealed that EMMPRIN was expressed at both the invasive edge of lesions and the adjacent epidermis, where S100A9 was also strongly expressed. In epidermal-specific transgenic mice, tail vein-injected melanoma accumulated in skin expressing S100A9 but not S100A8. Together, our results establish EMMPRIN as a receptor for S100A9 and suggest the therapeutic use in targeting S100A9-EMMPRIN interactions.

TIRAP, an adaptor protein for TLR2/4, transduces a signal from RAGE phosphorylated upon ligand binding.

The receptor for advanced glycation end products (RAGE) is thought to be involved in the pathogenesis of a broad range of inflammatory, degenerative and hyperproliferative diseases. It binds to diverse ligands and activates multiple intracellular signaling pathways. Despite these pivotal functions, molecular events just downstream of ligand-activated RAGE have been surprisingly unknown. Here we show that the cytoplasmic domain of RAGE is phosphorylated at Ser391 by PKCζ upon binding of ligands. TIRAP and MyD88, which are known to be adaptor proteins for Toll-like receptor-2 and -4 (TLR2/4), bound to the phosphorylated RAGE and transduced a signal to downstream molecules. Blocking of the function of TIRAP and MyD88 largely abrogated intracellular signaling from ligand-activated RAGE. Our findings indicate that functional interaction between RAGE and TLRs coordinately regulates inflammation, immune response and other cellular functions.

Changes of cell-surface thiols and intracellular signaling in human monocytic cell line THP-1 treated with diphenylcyclopropenone.

Changes of cell-surface thiols induced by chemical treatment may affect the conformations of membrane proteins and intracellular signaling mechanisms. In our previous study, we found that a non-toxic dose of diphenylcyclopropene (DPCP), which is a potent skin sensitizer, induced an increase of cell-surface thiols in cells of a human monocytic cell line, THP-1. Here, we examined the influence of DPCP on intracellular signaling. First, we confirmed that DPCP induced an increase of cell-surface thiols not only in THP-1 cells, but also in primary monocytes. The intracellular reduced-form glutathione/oxidized-form glutathione ratio (GSH/GSSG ratio) was not affected by DPCP treatment. By means of labeling with a membrane-impermeable thiol-reactive compound, Alexa Fluor 488 C5 maleimide (AFM), followed by two-dimensional gel electrophoresis and analysis by liquid chromatography coupled with electrospray tandem mass spectrometry (LC/MS/MS), we identified several proteins whose thiol contents were modified in response to DPCP. These proteins included cell membrane components, such as actin and ß-tubulin, molecular chaperones, such as heat shock protein 27A and 70, and endoplasmic reticulum (ER) stress-inducible proteins. Next, we confirmed the expression in DPCP-treated cells of spliced XBP1, a known marker of ER stress. We also detected the phosphorylation of SAPK/JNK and p38 MAPK, which are downstream signaling molecules in the IRE1α-ASK1 pathway, which is activated by ER stress. These data suggested that increase of cell-surface thiols might be associated with activation of ER stress-mediated signaling.

Multidimensional LC separations in shotgun proteomics.

Two modes of separation coupled with MS enable researchers to study complicated biological structures.

Motif-specific sampling of phosphoproteomes.

Phosphoproteomics, the targeted study of a subfraction of the proteome which is modified by phosphorylation, has become an indispensable tool to study cell signaling dynamics. We described a methodology that linked phosphoproteome and proteome analysis based on Ba2+ binding properties of amino acids. This technology selected motif-specific phosphopeptides independent of the system under analysis. MudPIT (Multidimensional Identification Technology) identified 1037 precipitated phosphopeptides from as little as 250 microg of proteins. To extend coverage of the phosphoproteome, we sampled the nuclear extract of HeLa cells with three values of Ba2+ ions molarity. The presence of more than 70% of identified phosphoproteins was further substantiated by their nonmodified peptides. Upon isoproterenol stimulation of HEK cells, we identified an increasing number of phosphoproteins from MAPK cascades and AKAP signaling hubs. We quantified changes in both protein and phosphorylation levels of 197 phosphoproteins including a critical kinase, MAPK1. Integration of differential phosphorylation of MAPK1 with knowledge bases constructed modules that correlated well with its role as node in cross-talk of canonical pathways.

Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data.

We investigated and compared three approaches for shotgun protein identification by combining MS and MS/MS information using LTQ-Orbitrap high mass accuracy data. In the first approach, we employed a unique mass identifier method where MS peaks matched to peptides predicted from proteins identified from an MS/MS database search are first subtracted before using the MS peaks as unique mass identifiers for protein identification. In the second method, we used an accurate mass and time tag method by building a potential mass and retention time database from previous MudPIT analyses. For the third method, we used a peptide mass fingerprinting-like approach in combination with a randomized database for protein identification. We show that we can improve protein identification sensitivity for low-abundance proteins by combining MS and MS/MS information. Furthermore, "one-hit wonders" from MS/MS database searching can be further substantiated by MS information and the approach improves the identification of low-abundance proteins. The advantages and disadvantages for the three approaches are then discussed.

A novel melanin inhibitor: hydroperoxy traxastane-type triterpene from flowers of Arnica montana.

We isolated a novel inhibitor of melanin biosynthesis from the flowers of Arnica montana L. (Compositae), and identified it as a traxastane-type triterpene (3beta,16beta-dihydroxy-21alpha-hydroperoxy-20(30)-taraxastene) [1] by means of 1D or 2D-NMR and liquid chromatography/high-resolution mass spectrometry (LC-HR-MS). Compound [1] at the concentration of 0.53 muM completely inhibited melanin accumulation in cultured B16 melanoma cells. It is one of the most potent among known plant inhibitors of melanin biosynthesis in cultured cells, being 50 times more potent than 4-methoxyphenol, which is used as an anti-pigmentation agent. Its mechanism of action is considered to involve inhibition of transcriptional factor MITF-M (melanocyte-type isoform of microphthalmia-associated transcription factor), which would lead to a decrease of tyrosinase and related genes. We confirmed that compound [1] decreased the protein levels of tyrosinase and its related proteins in B16 melanoma cells. Further study revealed that a similar hydroperoxy triterpene also suppressed the melanin pigment accumulation of B16 melanoma cells. These results indicate that the hydroperoxy group may play an important role in the suppression of the melanin accumulation by compound [1].

Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides.

Shotgun proteomics typically uses multidimensional LC/MS/MS analysis of enzymatically digested proteins, where strong cation-exchange (SCX) and reversed-phase (RP) separations are coupled to increase the separation power and dynamic range of analysis. Here we report an on-line multidimensional LC method using an anion- and cation-exchange mixed bed for the first separation dimension. The mixed-bed ion-exchange resin improved peptide recovery over SCX resins alone and showed better orthogonality to RP separations in two-dimensional separations. The Donnan effect, which was enhanced by the introduction of fixed opposite charges in one column, is proposed as the mechanism responsible for improved peptide recovery by producing higher fluxes of salt cations and lower populations of salt anions proximal to the SCX phase. An increase in orthogonality was achieved by a combination of increased retention for acidic peptides and moderately reduced retention of neutral to basic peptides by the added anion-exchange resin. The combination of these effects led to approximately 100% increase in the number of identified peptides from an analysis of a tryptic digest of a yeast whole cell lysate. The application of the method to phosphopeptide-enriched samples increased by 94% phosphopeptide identifications over SCX alone. The lower pKa of phosphopeptides led to specific enrichment in a single salt step resolving acidic phosphopeptides from other phospho- and non-phosphopeptides. Unlike previous methods that use anion exchange to alter selectivity or enrich phosphopeptides, the proposed format is unique in that it works with typical acidic buffer systems used in electrospray ionization, making it feasible for online multidimensional LC/MS/MS applications.

Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples.

Multidimensional separation is one of the most successful approaches for proteomics studies that deal with complex samples. We have developed an automated ultra-high-pressure multidimensional liquid chromatography system that operates up to approximately 20 kpsi to improve separations and increase protein coverage from limited amount of samples. The reversed-phase gradient is operated in the constant-flow mode opposed to the constant-pressure mode, which is typical of previous ultra-high-pressure systems. In contrast to constant-pressure systems, the gradient shape is fully controllable and can be optimized for the type of samples to be run. The system also features fast sample loading/desalting using a vented column approach to improve sample throughput. This approach was validated on a soluble fraction from yeast lysate where we achieved approximately 30% more protein identifications using a 60-cm-long triphasic capillary column than with our traditional approach. Advantages of the use of a relatively long reversed-phase column (approximately 50 cm) for MudPIT-type experiments are also discussed.