Mining Phosphopeptide Signals in Liquid Chromatography−Mass Spectrometry Data for Protein Phosphorylation Analysis

Moonlighting glyceraldehyde-3-phosphate dehydrogenase (GAPDH) protein of Lactobacillus gasseri attenuates allergic asthma via immunometabolic change in macrophages

BACKGROUND

The extra-intestinal effects of probiotics for preventing allergic diseases are well known. However, the probiotic components that interact with host target molecules and have a beneficial effect on allergic asthma remain unknown. Lactobacillus gasseri attenuates allergic airway inflammation through the activation of peroxisome proliferator- activated receptor γ (PPARγ) in dendritic cells. Therefore, we aimed to isolate and investigate the immunomodulatory effect of the PPARγ activation component from L. gasseri.

METHODS

Culture supernatants of L. gasseri were fractionated and screened for the active component for allergic asthma. The isolated component was subjected to in vitro functional assays and then cloned. The crystal structure of this component protein was determined using X-ray crystallography. Intrarectal inoculation of the active component-overexpressing Clear coli (lipopolysaccharide-free Escherichia coli) and intraperitoneal injection of recombinant component protein were used in a house dust mite (HDM)-induced allergic asthma mouse model to investigate the protective effect. Recombinant mutant component proteins were assayed, and their structures were superimposed to identify the detailed mechanism of alleviating allergic inflammation.

RESULTS

A moonlighting protein, glycolytic glyceraldehyde 3-phosphate dehydrogenase (GAPDH), LGp40, that has multifunctional effects was purified from cultured L. gasseri, and the crystal structure was determined. Both intrarectal inoculation of LGp40-overexpressing Clear coli and intraperitoneal administration of recombinant LGp40 protein attenuated allergic inflammation in a mouse model of allergic asthma. However, CDp40, GAPDH isolated from Clostridium difficile did not possess this anti-asthma effect. LGp40 redirected allergic M2 macrophages toward the M1 phenotype and impeded M2-prompted Th2 cell activation through glycolytic activity that induced immunometabolic changes. Recombinant mutant LGp40, without enzyme activity, showed no protective effect against HDM-induced airway inflammation.

CONCLUSIONS

We found a novel mechanism of moonlighting LGp40 in the reversal of M2-prompted Th2 cell activation through glycolytic activity, which has an important immunoregulatory role in preventing allergic asthma. Our results provide a new strategy for probiotics application in alleviating allergic asthma.

Quantitative phosphoproteomics reveals the effect of baeSR and acrB genes on protein phosphorylation in Salmonella enterica serovar Typhimurium

The BaeSR two-component system and the AcrB efflux pump are closely associated with Salmonella resistance to antibiotics. However, the relationship between the two-component system, efflux pumps and protein phosphorylation of Salmonella is poorly understood. In this study, S. typhimurium ciprofloxacin-resistant strain CR, baeSR gene deletion strain CR^ΔbaeSR, acrB gene deletion strain CR^ΔacrB, and double gene deletion strain CR^{ΔbaeSRΔacrB} were used to explore phosphorylated proteins with significant difference, based on non-marker, quantitative phosphorylation modified proteomics technique. Consequently, 363 phosphosites of 213 phosphoproteins were identified in the four strains. More than 70% of the phosphosites were serine phosphorylation. In the CR^ΔbaeSR/CR, CR^ΔacrB/CR and CR^{ΔbaeSRΔacrB}/CR comparison groups, 36, 37 and 49 phosphosites were significantly altered, respectively. Bioinformatic analysis revealed that the main enrichment pathways of these differentially phosphorylated proteins were metabolic pathways, biosynthesis of antibiotics, phosphotransferase system (PTS), ABC transporters, and lipopolysaccharide biosynthesis. Furthermore, 21 differentially phosphorylated proteins were identified to be associated with antibiotic resistance. These results suggest that the BaeSR two-component system and the AcrB efflux pump affect the phosphorylation of proteins in S. typhimurium and may influence the drug resistance and virulence of S. typhimurium by affecting protein phosphorylation, providing a new idea to explore the mechanism of drug resistance in Salmonella.

Functional kinomics establishes a critical node of volume-sensitive cation-Cl- cotransporter regulation in the mammalian brain

Cell volume homeostasis requires the dynamically regulated transport of ions across the plasmalemma. While the ensemble of ion transport proteins involved in cell volume regulation is well established, the molecular coordinators of their activities remain poorly characterized. We utilized a functional kinomics approach including a kinome-wide siRNA-phosphoproteomic screen, a high-content kinase inhibitor screen, and a kinase trapping-Orbitrap mass spectroscopy screen to systematically identify essential kinase regulators of KCC3 Thr991/Thr1048 phosphorylation - a key signaling event in cell swelling-induced regulatory volume decrease (RVD). In the mammalian brain, we found the Cl--sensitive WNK3-SPAK kinase complex, required for cell shrinkage-induced regulatory volume decrease (RVI) via the stimulatory phosphorylation of NKCC1 (Thr203/Thr207/Thr212), is also essential for the inhibitory phosphorylation of KCC3 (Thr991/Thr1048). This is mediated in vivo by an interaction between the CCT domain in SPAK and RFXV/I domains in WNK3 and NKCC1/KCC3. Accordingly, genetic or pharmacologic WNK3-SPAK inhibition prevents cell swelling in response to osmotic stress and ameliorates post-ischemic brain swelling through a simultaneous inhibition of NKCC1-mediated Cl- uptake and stimulation of KCC3-mediated Cl- extrusion. We conclude that WNK3-SPAK is an integral component of the long-sought "Cl-/volume-sensitive kinase" of the cation-Cl- cotransporters, and functions as a molecular rheostat of cell volume in the mammalian brain.

Identification of Phosphorylated Cyclin-Dependent Kinase 1 Associated with Colorectal Cancer Survival Using Label-Free Quantitative Analyses

Colorectal cancer is the most common form of cancer in the world, and the five-year survival rate is estimated to be almost 90% in the early stages. Therefore, the identification of potential biomarkers to assess the prognosis of early stage colorectal cancer patients is critical for further clinical treatment. Dysregulated tyrosine phosphorylation has been found in several diseases that play a significant regulator of signaling in cellular pathways. In this study, this strategy was used to characterize the tyrosine phosphoproteome of colorectal cell lines with different progression abilities (SW480 and SW620). We identified a total of 280 phosphotyrosine (pTyr) peptides comprising 287 pTyr sites from 261 proteins. Label-free quantitative analysis revealed the differential level of a total of 103 pTyr peptides between SW480 and SW620 cells. We showed that cyclin-dependent kinase I (CDK1) pTyr15 level in SW480 cells was 3.3-fold greater than in SW620 cells, and these data corresponded with the label-free mass spectrometry-based proteomic quantification analysis. High level CDK1 pTyr15 was associated with prolonged disease-free survival for stage II colorectal cancer patients (n = 79). Taken together, our results suggest that the CDK1 pTyr15 protein is a potential indicator of the progression of colorectal cancer.

Screening for protein phosphorylation using nanoscale reactions on microdroplet arrays

We present a novel and straightforward screening method to detect protein phosphorylations in complex protein mixtures. A proteolytic digest is separated by a conventional nanoscale liquid chromatography (nano-LC) separation and the eluate is immediately compartmentalized into microdroplets, which are spotted on a microarray MALDI plate. Subsequently, the enzyme alkaline phosphatase is applied to every second microarray spot to remove the phosphate groups from phosphorylated peptides, which results in a mass shift of n×-80 Da. The MALDI-MS scan of the microarray is then evaluated by a software algorithm to automatically identify the phosphorylated peptides by exploiting the characteristic chromatographic peak profile induced by the phosphatase treatment. This screening method does not require extensive MS/MS experiments or peak list evaluation and can be easily extended to other enzymatic or chemical reactions.

iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation

Background

Comprehensive characterization of the phosphoproteome in living cells is critical in signal transduction research. But the low abundance of phosphopeptides among the total proteome in cells remains an obstacle in mass spectrometry-based proteomic analysis. To provide a solution, an alternative analytic strategy to confidently identify phosphorylated peptides by using the alkaline phosphatase (AP) treatment combined with high-resolution mass spectrometry was provided. While the process is applicable, the key integration along the pipeline was mostly done by tedious manual work.

Results

We developed a software toolkit, iPhos, to facilitate and streamline the work-flow of AP-assisted phosphoproteome characterization. The iPhos tookit includes one assister and three modules. The iPhos Peak Extraction Assister automates the batch mode peak extraction for multiple liquid chromatography mass spectrometry (LC-MS) runs. iPhos Module-1 can process the peak lists extracted from the LC-MS analyses derived from the original and dephosphorylated samples to mine out potential phosphorylated peptide signals based on mass shift caused by the loss of some multiples of phosphate groups. And iPhos Module-2 provides customized inclusion lists with peak retention time windows for subsequent targeted LC-MS/MS experiments. Finally, iPhos Module-3 facilitates to link the peptide identifications from protein search engines to the quantification results from pattern-based label-free quantification tools. We further demonstrated the utility of the iPhos toolkit on the data of human metastatic lung cancer cells (CL1-5).

Conclusions

In the comparison study of the control group of CL1-5 cell lysates and the treatment group of dasatinib-treated CL1-5 cell lysates, we demonstrated the applicability of the iPhos toolkit and reported the experimental results based on the iPhos-facilitated phosphoproteome investigation. And further, we also compared the strategy with pure DDA-based LC-MS/MS phosphoproteome investigation. The results of iPhos-facilitated targeted LC-MS/MS analysis convey more thorough and confident phosphopeptide identification than the results of pure DDA-based analysis.

Optimization of titanium dioxide and immunoaffinity-based enrichment procedures for tyrosine phosphopeptide using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Tyrosine phosphorylation is an important regulator of signaling in cellular pathways, and dysregulated tyrosine phosphorylation causes several diseases. Mass spectrometry has revealed the importance of global phosphoproteomic characterization. Analysis of tyrosine phosphorylation by studying the mass-spectrometry (MS)-determined phosphoproteome remains difficult because of the relatively low abundance of tyrosine phosphoproteins. To effectively evaluate tyrosine-phosphopeptide enrichment and reduce ion suppression from non-phosphorylated peptides in MS analysis, three trypsin-digested BSA peptides and 14 standard phosphopeptides, including six tyrosine phosphopeptides, four serine phosphopeptides, and four threonine phosphopeptides, were subjected to titanium dioxide immunoaffinity-based enrichment and also to combined enrichment using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-mass spectrometry (LC-MS) analyses. The enrichment factors were evaluated to determine the efficiency of each enrichment procedure. Comparison of five optimized enrichment methods, including TiO2-based immunoaffinity purification in Tris and MOPS buffer systems, TiO2-immunoaffinity enrichment, and immunoaffinity-TiO2 enrichment for total tyrosine, serine and threonine phosphopeptides, revealed that the order of the enrichment factors for total tyrosine phosphopeptides is: (i) immunoaffinity-TiO2 (enrichment factor = 38,244), (ii) TiO2-immunoaffinity (enrichment factor = 24,987), (iii) TiO2 micro-column (enrichment factor = 10,305), (iv) immunoaffinity in Tris buffer system (enrichment factor = 1450), and (v) immunoaffinity in the MOPS buffer system (enrichment factor = 32). These results reveal that an alternative enrichment scheme before use of a TiO2 micro-column, using immunoaffinity 4G10 and PY99 antibody enrichment under optimized conditions, can provide greater selectivity for tyrosine-phosphopeptide enrichment.

Phosphoproteomic analyses reveal that galectin-1 augments the dynamics of B-cell receptor signaling

B-cell activation is important for mounting humoral immune responses and antibody production. Galectin-1 has multiple regulatory functions in immune cells. However, the effects of galectin-1 modulation and the mechanisms underlying the coordination of B-cell activation are unclear. To address this issue, we applied label-free quantitative phosphoproteomic analysis to investigate the dynamics of galectin-1-induced signaling in comparison with that following anti-IgM treatment. A total of 3247 phosphorylation sites on 1245 proteins were quantified, and 70-80% of the 856 responsive phosphoproteins were commonly activated during various biological functions. The similarity between galectin-1- and anti-IgM-elicited B-cell receptor (BCR) signaling pathways was also revealed. Additionally, the mapping of the 149 BCR-responsive phosphorylation sites provided complementary knowledge of BCR signaling. Compared to anti-IgM induction, the phosphoproteomic profiling of BCR signaling, along with validation by western blot analysis and pharmacological inhibitors, revealed that the activation of Syk, Btk, and PI3K may be dominant in galectin-1-mediated activation. We further demonstrated that the proliferation of antigen-primed B cells was diminished in the absence of galectin-1 in an animal model. Together, these findings provided evidence for a new role and insight into the mechanism of how galectin-1 augments the strength of the immunological synapse by modulating BCR signaling.

BIOLOGICAL SIGNIFICANCE

The current study revealed the first systematic phosphorylation-mediated signaling network and its dynamics in B cell activation. The comparative phosphoproteomic analysis on the dynamics of galectin-1 induced activation profiles not only showed that exogenously added galectin-1 augmented B-cell activation but also revealed its relatively enhanced activation in PI3K pathway. Together with proliferation assay, we further delineated that galectin-1 is important for B-cell proliferation in response to antigen challenge. Our phosphoproteomic study reveals a new role for galectin-1 in augmenting the strength of immunological synapse by modulating BCR signaling.

Characterization of the Phosphoproteome in SLE Patients

Protein phosphorylation is a complex regulatory event that is involved in the signaling networks that affect virtually every cellular process. The protein phosphorylation may be a novel source for discovering biomarkers and drug targets. However, a systematic analysis of the phosphoproteome in patients with SLE has not been performed. To clarify the pathogenesis of systemic lupus erythematosus (SLE), we compared phosphoprotein expression in PBMCs from SLE patients and normal subjects using proteomics analyses. Phosphopeptides were enriched using TiO₂ from PBMCs isolated from 15 SLE patients and 15 healthy subjects and then analyzed by automated LC-MS/MS analysis. Phosphorylation sites were identified and quantitated by MASCOT and MaxQuant. A total of 1035 phosphorylation sites corresponding to 618 NCBI-annotated genes were identified in SLE patients compared with normal subjects. Differentially expressed proteins, peptides and phosphorylation sites were then subjected to bioinformatics analyses. Gene ontology(GO) and pathway analyses showed that nucleic acid metabolism, cellular component organization, transport and multicellular organismal development pathways made up the largest proportions of the differentially expressed genes. Pathway analyses showed that the mitogen-activated protein kinase (MAPK) signaling pathway and actin cytoskeleton regulators made up the largest proportions of the metabolic pathways. Network analysis showed that rous sarcoma oncogene (SRC), v-rel reticuloendotheliosis viral oncogene homolog A (RELA), histone deacetylase (HDA1C) and protein kinase C, delta (PRKCD) play important roles in the stability of the network. These data suggest that aberrant protein phosphorylation may contribute to SLE pathogenesis.

A statistical procedure to selectively detect metabolite signals in LC-MS data based on using variable isotope ratios

The tracing of metabolite signals in LC-MS data using stable isotope-labeled compounds has been described in the literature. However, the filtering efficiency and confidence when mining metabolite signals in complex LC-MS datasets can be improved. Here, we propose an additional statistical procedure to increase the compound-derived signal mining efficiency. This method also provides a highly confident approach to screen out metabolite signals because the correlation of varying concentration ratios of native/stable isotope-labeled compounds and their instrumental response ratio is used. An in-house computational program [signal mining algorithm with isotope tracing (SMAIT)] was developed to perform the statistical procedure. To illustrate the SMAIT concept and its effectiveness for mining metabolite signals in LC-MS data, the plasticizer, di-(2-ethylhexyl) phthalate (DEHP), was used as an example. The statistical procedure effectively filtered 15 probable metabolite signals from 3617 peaks in the LC-MS data. These probable metabolite signals were considered structurally related to DEHP. Results obtained here suggest that the statistical procedure could be used to confidently facilitate the detection of probable metabolites from a compound-derived precursor presented in a complex LC-MS dataset.

Combining alkaline phosphatase treatment and hybrid linear ion trap/Orbitrap high mass accuracy liquid chromatography-mass spectrometry data for the efficient and confident identification of protein phosphorylation

Protein phosphorylation is a vital post-translational modification that is involved in a variety of biological processes. Several mass spectrometry-based methods have been developed for phosphoprotein characterization. In our previous work, we demonstrated the capability of a computational algorithm in mining phosphopeptide signals in large LC-MS data sets by measuring the mass shifts due to phosphatase treatment (Wu, H. Y.; Tseng, V. S.; Liao, P. C. J. Proteome Res. 2007, 6, 1812-1821). Mass accuracy seems to play an important role in efficiently selecting out phosphopeptide signals. In recent years, the hybrid linear ion trap (LTQ)/Orbitrap mass spectrometer, which provides a high mass accuracy, has emerged as a powerful instrument in proteomic analysis. Here, we developed a process to incorporate LC-MS data that was generated from an LTQ/Orbitrap mass spectrometer into our strategy for taking advantage of the accurate mass measurement. LTQ/Orbitrap raw files were converted to the open file format mzXML via the ReAdW.exe program. To find peaks that were contained in each mzXML file, an open-source computer program, msInspect, was utilized to locate isotopes and assemble those isotopes into peptides. An in-house program, LcmsFormatConverter, was utilized for signal filtering and format transformation. A proposed in-house program, DeltaFinder, was modified and used for defining signals with an exact mass shift due to the dephosphorylation reaction, which generated a table that listed potential phosphopeptide signals. The retention times and m/z values of these selected LC-MS signals were used to program subsequent LC-MS/MS experiments to get high-confidence phosphorylation site determination. Compared to our previous work finished by using a quadrupole/time-of-flight mass spectrometer, a larger number of phosphopeptides in the casein mixture were identified by using LTQ/Orbitrap data, demonstrating the merit of high mass accuracy in our strategy. In addition, the characterization of the lung cancer cell tyrosine phosphoproteome revealed that the use of alkaline phosphatase treatment combined with accurate mass measurement in this strategy increased data repeatability and confidence.

Strategy for determination of in vitro protein acetylation sites by using isotope-labeled acetyl coenzyme A and liquid chromatography-mass spectrometry

Acetylation of proteins on specific lysine residues by acetyltransferase enzymes is a post-translational modification for biologically relevant regulation. In this study, we proposed a strategy to determine the in vitro acetylation sites of proteins by tracing isotope-labeled acetyl groups using mass spectrometry. Isotope-labeled and unlabeled acetyl groups transferred onto the substrates in vitro result in a specific "mass difference" that can be measured by MS analysis and utilized for localization of potential acetylated peptide signals. The identification of acetylation site is facilitated by conducting MS/MS experiments on those selected signals. Acetylation reactions of substrates were performed in the presence of acetyltransferase and equal molar of isotope-labeled acetyl coenzyme A ([(13)C2-2-D3]-acetyl-CoA) and unlabeled acetyl-CoA. After enzymatic digestion, the resulting peptide mixture was fractionated by off-line, reversed-phase high-pressure liquid chromatography and the accurate mass measurement of peptides was achieved by a quadrupole/time-of-flight mass spectrometer. Signals with 5-Da (or their multiples) mass differences and equal responses were selected out by program computation. Those potential acetylated peptide signals were subjected to MS/MS analyses for determination of acetylation sites. We have used histone H3 peptide (aa 1-20), histone H2B peptide (aa 1-21), histone H2A, and histone H2B proteins as the model compounds to demonstrate the applicability of this analytical scheme for the characterization of in vitro acetylation sites.

Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search

We developed a probability-based machine-learning program, Colander, to identify tandem mass spectra that are highly likely to represent phosphopeptides prior to database search. We identified statistically significant diagnostic features of phosphopeptide tandem mass spectra based on ion trap CID MS/MS experiments. Statistics for the features are calculated from 376 validated phosphopeptide spectra and 376 nonphosphopeptide spectra. A probability-based support vector machine (SVM) program, Colander, was then trained on five selected features. Data sets were assembled both from LC/LC-MS/MS analyses of large-scale phosphopeptide enrichments from proteolyzed cells, tissues and synthetic phosphopeptides. These data sets were used to evaluate the capability of Colander to select pS/pT-containing phosphopeptide tandem mass spectra. When applied to unknown tandem mass spectra, Colander can routinely remove 80% of tandem mass spectra while retaining 95% of phosphopeptide tandem mass spectra. The program significantly reduced computational time spent on database search by 60-90%. Furthermore, prefiltering tandem mass spectra representing phosphopeptides can increase the number of phosphopeptide identifications under a predefined false positive rate.

An efficient method for dephosphorylation of phosphopeptides by cerium oxide

In this article, an effective method for dephosphorylation of phosphopeptides by cerium oxide is described. The dephosphorylation activity of cerium oxide was evaluated by two standard phosphopeptides and the phosphopeptides in digests of phosphoprotein alpha-casein and beta-casein. Results showed that the dephosphorylation of all the phosphopeptides was completed in 10 min, and temperature had little effect on the dephosphorylation, the dephosphorylation could be carried out at 0 degrees C, room temperature and 37 degrees C. The dephosphorylation mediated by cerium oxide can be attributed to Lewis acid and nucleophile activations. Advantages of using cerium oxide as catalyst for the dephosphorylation include: safe, simple, high catalytic activity, and no precise control of the treatment temperature. The method is valid for the phosphorylation of Ser, Thr and Tyr, and can be used for phosphoprotein analysis.

Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: application to cell signaling events of interferon-gamma-stimulated macrophages

Protein phosphorylation is a central cell signaling event that underlies a broad spectrum of key physiological processes. Advances in affinity chromatography and mass spectrometry are now providing the ability to identify and quantitate thousands of phosphorylation sites simultaneously. Comprehensive phosphoproteome analyses present sizable analytical challenges in view of suppression effects of phosphopeptides and the variable quality of MS/MS spectra. This work presents an integrated enzymatic and data mining approach enabling the comprehensive detection of native and putative phosphopeptides following alkaline phosphatase digestion of titanium dioxide (TiO2)-enriched cell extracts. The correlation of retention times of more than 750 phospho- and dephosphopeptide pairs from J774 macrophage cell extracts indicated that removal of the phosphate groups can impart a gain or a loss in hydrophobicity that is partly explained by the formation of a salt bridge with proximal amino groups. Dephosphorylation also led to an average 2-fold increase in MS sensitivity that facilitated peptide sequencing. More importantly, alkaline phosphatase digestion enhanced the overall population of putative phosphopeptides from TiO2-enriched cell extracts providing a unique approach to profile multiphosphorylated cognates that would have remained otherwise undetected. The application of this approach is demonstrated for differential phosphoproteome analyses of mouse macrophages exposed to interferon-gamma for 5 min. TiO2 enrichment enabled the identification of 1143 phosphopeptides from 432 different proteins of which 125 phosphopeptides showed a 2-fold change upon interferon-gamma exposure. The use of alkaline phosphatase nearly doubled the number of putative phosphopeptides assignments leading to the observation of key interferon-gamma signaling events involved in vesicle trafficking, production of reactive oxygen species, and mRNA translation.