Tag‐Convertible Photocrosslinker with Click‐On/Off N‐Acylsulfonamide Linkage for Protein Identification

The N‐acylsulfonamide group, known as a safety‐catch linker, has been applied to photoaffinity labeling (PAL) using a cinnamate‐type photocrosslinker to improve the efficiency of PAL‐based target identification. A bioorthogonal sulfo‐click reaction was used to stably link a photocrosslinker unit with N‐acylsulfonamide linkage to produce a photoactivatable probe without any protection. In addition, the crosslinked protein was selectively isolated with a small cinnamate tag via linkage disruption upon N‐alkylation. Furthermore, the tag moiety was photochemically converted to a stable coumarin derivative by losing a water molecule, which is a useful property in MS‐based identification.     

Photoinduced Electron Transfer‐Regulated Protein Labeling With a Coumarin‐Based Multifunctional Photocrosslinker

We developed a novel diazirine‐based photolabeling agent having a (coumarin‐4‐yl)methyl ester scaffold, which exhibited multiple photochemical properties of crosslinking, fluorogenicity and cleavage. These properties can be kinetically regulated via photoinduced electron transfer between diazirine and coumarin moieties. The C?O bond of (coumarin‐4‐yl)methyl ester can be cleaved via photochemical excitation of coumarin moiety, that function has been initially quenched by the diazirine moiety. Upon diazirine photolysis with 365‐nm light, interacting protein was stably captured with photoactivatable ligand probe. Then, the unlocked cleavage function was activated with 313 nm light, and the reaction was accelerated in a weakly‐basic solution. The crosslinked protein could be selectively isolated with attachment of a small coumarin tag on the surface. This multi‐functional labeling agent has a great potential to facilitate LC‐MS/MS‐based protein identification.     

Quantification of intact covalently metal labeled proteins using ESI‐MS/MS

Mass spectrometric methods matured from the successful qualitative characterization of proteins in complex mixtures into methods for quantitative proteomics often based on chemical tags with stable isotope labeling. In the study presented here, we extended the application of lanthanide‐ion‐based tags from the quantification using inductively coupled plasma‐MS into the quantification of labeled intact proteins using electrospray ionization (ESI)‐MS and ESI‐MS/MS. We applied the metal chelate tag MeCAT‐iodoacetamide (IA) (1,4,7,10‐tetraazacyclododecane N,N′,N″,N″ ′‐tetra acetic acid with a IA reactive site). Labeled proteins were separated using C3‐reversed phase‐high‐performance liquid chromatography interfaced to ESI‐MS. We could prove that even large proteins were completely labeled at all available cysteine residues using MeCAT‐IA with only a small excess of reagent. Fragmentation of labeled proteins either using infrared multiphoton dissociation in Fourier transform ion cyclotron resonance‐MS or higher‐energy collision dissociation with an Orbitrap gave characteristic fragments. We used these fragments to quantify several intact proteins avoiding digestion. To demonstrate the applicability, human serum albumin was quantified in blood serum. The high‐performance liquid chromatography/ESI‐MS/MS quantification data were validated using inductively coupled plasma‐MS. Because the metal within the tag may be any of the lanthanides, multiplexing capabilities are inherent. Copyright © 2014 John Wiley & Sons, Ltd.     

A proteomics method using immunoaffinity fluorogenic derivatization–liquid chromatography/tandem mass spectrometry (FD‐LC‐MS/MS) to identify a set of interacting proteins

Biological functions in organisms are usually controlled by a set of interacting proteins, and identifying the proteins that interact is useful for understanding the mechanism of the functions. Immunoprecipitation is a method that utilizes the affinity of an antibody to isolate and identify the proteins that have interacted in a biological sample. In this study, the FD‐LC–MS/MS method, which involves fluorogenic derivatization followed by separation and quantification by HPLC and finally identification of proteins by HPLC–tandem mass spectrometry, was used to identify proteins in immunoprecipitated samples, using heat shock protein 90 (HSP90) as a model of an interacting protein in HepaRG cells. As a result, HSC70 protein, which was known to form a complex with HSP90, was isolated, together with three different types of HSP90‐beta. The results demonstrated that the proposed immunoaffinity–FD‐LC–MS/MS method could be useful for simultaneously detecting and identifying the proteins that interact with a certain protein.     

3‐Mercapto‐2,6‐Pyridinedicarboxylic Acid: A Small Lanthanide‐Binding Tag for Protein Studies by NMR Spectroscopy

Paramagnetic effects from lanthanide ions present powerful tools for protein studies by nuclear magnetic resonance (NMR) spectroscopy provided that the lanthanide can be site‐specifically and rigidly attached to the protein. A new, particularly small and rigid lanthanide‐binding tag, 3‐mercapto‐2,6‐pyridinedicarboxylic acid (3MDPA), was synthesized and attached to two different proteins via a disulfide bond. The complexes of the N‐terminal domain of the E. coli arginine repressor (ArgN) with seven different paramagnetic lanthanide ions and Co²⁺ were analyzed in detail by NMR spectroscopy. The magnetic susceptibility anisotropy (Δχ) tensors and metal position were determined from pseudocontact shifts. The 3MDPA tag generated very different Δχ tensor orientations compared to the previously studied 4‐mercaptomethyl‐DPA tag, making it a highly complementary and useful tool for protein NMR studies.     

MALDI‐TOF‐Massenspektrometrie: Risikoanalyse im Flug

The high accuracy, molecular resolution and sensitivity of matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) make it an efficient method for analysing all kinds of biomolecules including nucleic acids, proteins/peptides, carbohydrates and lipids. MALDI‐TOF‐MS based high‐throughput genotyping of genetic heterogeneities possesses the potential of becoming a routine method. MAL‐DI‐TOF‐MS can be used for the identification of proteins and posttranslational modifications. Taken together, MALDI‐TOF‐MS represents a integrated platform technology in bioanalytics and molecular medicine.     

Easy‐to‐Attach/Detach Solubilizing‐Tag‐Aided Chemical Synthesis of an Aggregative Capsid Protein

A solubilizing Trt‐K₁₀ tag was developed for the effective chemical preparation of peptides/proteins with low solubility. The Trt‐K₁₀ tag comprises a hydrophilic oligo‐Lys sequence and a trityl anchor, and can be selectively introduced to a side chain thiol of Cys of deprotected peptides/proteins with a trityl alcohol‐type introducing reagent Trt(OH)‐K₁₀ under acidic conditions. Significantly, the ligation product in the reaction mixture of a thiol‐additive‐free native chemical ligation can be modified directly in a one‐pot manner to facilitate the isolation of the product by high‐performance liquid chromatography. Finally, the Trt‐K₁₀ tag can be readily removed with a standard trifluoroacetic acid cocktail. Using this easy‐to‐attach/detach tag‐aided method, a hepatitis B virus capsid protein that is usually difficult to handle was synthesized successfully.     

Improved conditions for fluorescent staining of proteins with 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid in SDS‐PAGE

A simple and sensitive fluorescent staining method for the detection of proteins in SDS‐PAGE, namely IB (improved 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid) stain, is described. Non‐covalent hydrophobic probe 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid was applied as a fluorescent dye, which can bind to hydrophobic sites in proteins non‐specifically. As low as 1 ng of protein band can be detected briefly by 30 min washing followed by 15 min staining without the aiding of stop or destaining step. The sensitivity of the new presented protocol is similar to that of SYPRO Ruby, which has been widely accepted in proteomic research. Comparative analysis of the MS compatibility of IB stain and SYPRO Ruby stain allowed us to address that IB stain is compatible with the downstream of protein identification by PMF.     

Cysteine‐capped ZnSe quantum dots as affinity and accelerating probes for microwave enzymatic digestion of proteins via direct matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometric analysis

Fluorescent semiconductor quantum dots (QDs) exhibit great potential and capability for many biological and biochemical applications. We report a simple strategy for the synthesis of aqueous stable ZnSe QDs by using cysteine as the capping agent (ZnSe‐Cys QDs). The ZnSe QDs can act as affinity probes to enrich peptides and proteins via direct matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) analysis. This nanoprobe could significantly enhance protein signals (insulin, ubiquitin, cytochrome c, myoglobin and lysozyme) in MALDI‐TOFMS by 2.5–12 times compared with the traditional method. Additionally, the ZnSe‐Cys QDs can be applied as heat absorbers (as accelerating probes) to speed up microwave‐assisted enzymatic digestion reactions and also as affinity probes to enrich lysozyme‐digested products in MALDI‐TOFMS. Furthermore, after the enrichment experiments, the solutions of ZnSe‐Cys QDs mixed with proteins can be directly deposited onto the MALDI plates for rapid analysis. This approach shows a simple, rapid, efficient and straightforward method for direct analysis of proteins or peptides by MALDI‐TOFMS without the requirement for further time‐consuming separation processes, tedious washing steps or laborious purification procedures. The present study has demonstrated that ZnSe‐Cys QDs are reliable and potential materials for rapid, selective separation and enrichment of proteins as well as accelerating probes for microwave‐digested reactions for proteins than the regular MALDI‐MS tools. Additionally, we also believe that this work may also inspire investigations for applications of QDs in the field of MALDI‐MS for proteomics. Copyright © 2009 John Wiley & Sons, Ltd.     

CE‐ESI‐TOF/MS for human growth hormone analysis

CE is a powerful analytical tool used to separate intact biomolecules such as proteins. The coupling of CE with TOF/MS produces a very promising method that can be used to detect and identify proteins in different matrices. This paper describes an efficient, rapid, and simple CE‐ESI‐TOF/MS procedure for the analysis of endogenous human growth hormone and recombinant human growth hormone without sample preparation. Operational factors were optimized using an experimental design, and the method was successfully applied to distinguish human growth hormone and recombinant human growth hormone in unknown samples.     

Identification and characterization of cysteinyl exposure in proteins by selective mercury labeling and nano‐electrospray ionization quadrupole time‐of‐flight mass spectrometry

We describe a method for probing surface‐exposed cysteines in proteins by selective labeling with p‐hydroxymercuribenzoate (PMB) combined with nano‐electrospray ionization mass spectrometric analysis (nanoESI‐MS). The rapid, stoichiometric, and specific labeling by PMB of surface‐exposed cysteines allows for characterization of the accessibility of the cysteines using a single MS analysis. Moreover, by taking advantage of the large mass shift of 321 Da, unique isotopic pattern, and enhanced MS signal of PMB‐labeled cysteine‐containing peptide fragments, the surface‐exposed cysteines in proteins can be accurately identified by peptide mapping. The number and sites of reactive cysteines on the surface of human and rat hemoglobins (hHb and rHb) were identified as examples. Collision‐induced dissociation tandem mass spectrometric (MS/MS) analysis of specific peptides further confirmed the selective labeling of PMB in hHb. The subtle difference between the different cysteine residues in rHb was also evaluated by multiple PMB titrations. The difference between the two cysteines in their environment may partially explain their reaction specificity. Cysteine 125 in the β unit of rHb is exposed on the surface, explaining its reactivity with glutathione. Cysteine 13 in the α subunit of rHb is much less exposed, and is located in a hydrophobic pocket, a conclusion that is consistent with the previous observation of its selective binding with dimethylarsinous acid, a reactive arsenic metabolite. The method is potentially useful for probing cysteines in other biologically important proteins and for studying proteins that are associated with conformational or structural changes induced by denaturing processes, protein modifications, protein‐protein interactions and protein assemblies. Copyright © 2010 John Wiley & Sons, Ltd.     

Global quantification of phosphoproteins combining metabolic labeling and gel‐based proteomics in B. pumilus

Differential proteomics targeting the protein abundance is commonly used to follow changes in biological systems. Differences in localization and degree of post‐translational modifications of proteins including phosphorylations are of tremendous interest due to the anticipated role in molecular regulatory processes. Because of their particular low abundance in prokaryotes, identification and quantification of protein phosphorylation is traditionally performed by either comparison of spot intensities on two‐dimensional gels after differential phosphoprotein staining or gel‐free by stable isotope labeling, sequential phosphopeptide enrichment and following LC‐MS analysis. In the current work, we combined in a proof‐of‐principle experiment these techniques using ¹⁴N/¹⁵N metabolic labeling with succeeding protein separation on 2D gels. The visualization of phosphorylations on protein level by differential staining was followed by protein identification and determination of phosphorylation sites and quantification by LC‐MS/MS. This approach should avoid disadvantages of traditional workflows, in particular the limited capability of peptide‐based gel‐free methods to quantify isoforms of proteins. Comparing control and stress conditions allowed for relative quantification in protein phosphorylation in Bacillus pumilus exposed to hydrogen peroxide. Altogether, we quantified with this method 19 putatively phosphorylated proteins.     

Cleavable hydrophilic linker for one-bead-one-compound sequencing of oligomer libraries by tandem mass spectrometry

We have developed a method for the rapid and unambiguous identification of sequences of hit compounds from one-bead-one-compound combinatorial libraries of peptide and peptoid ligands. The approach uses a cleavable linker that is hydrophilic to help reduce nonspecific binding to biological samples and allows for the attachment of a halogen tag, which greatly facilitates post-screening sequencing by tandem mass spectrometry (MS/MS). The linker is based on a tartaric acid unit, which, upon cleavage from resin, generates a C-terminal aldehyde. This aldehyde can then be derivatized with a bromine-containing amino-oxy compound that serves as an isotope tag for subsequent MS/MS analysis of y-ion fragments. We have applied this linker and method to the syntheses of a number of peptoids that vary in sequence and length and have also demonstrated single-bead sequencing of a peptoid pentamer. The linker is also shown to have very low levels of nonspecific binding to proteins.     

Drug Target Identification Using Affinity Core‐Shell Magnetic Nanoparticles and Mass Spectrometry

Affinity core‐shell magnetic nanoparticles (MNPs) were prepared for identifying the target proteins of drugs in the cell lysate when used in combination with nano‐high‐performance liquid chromatography tandem mass spectrometry (HPLC‐MS/MS)‐based shotgun proteomic analysis. A number of new potential targets of cyclosporine A (CsA) could be identified, owing to the high efficacy of the affinity MNPs in drug target identification. To the best of our knowledge, this is the first time to reveal such an abundant target spectrum of CsA.     

Separation with zwitterionic hydrophilic interaction liquid chromatography improves protein identification by matrix‐assisted laser desorption/ionization‐based proteomic analysis

Comprehensive proteomic analyses necessitate efficient separation of peptide mixtures for the subsequent identification of proteins by mass spectrometry (MS). However, digestion of proteins extracted from cells and tissues often yields complex peptide mixtures that confound direct comprehensive MS analysis. This study investigated a zwitterionic hydrophilic interaction liquid chromatography (ZIC‐HILIC) technique for the peptide separation step, which was verified by subsequent MS analysis. Human serum albumin (HSA) was the model protein used for this analysis. HSA was digested with trypsin and resolved by ZIC‐HILIC or conventional strong cation exchange (SCX) prior to MS analysis for peptide identification. Separation with ZIC‐HILIC significantly improved the identification of HSA peptides over SCX chromatography. Detailed analyses of the identified peptides revealed that the ZIC‐HILIC has better peptide fractionation ability. We further demonstrated that ZIC‐HILIC is useful for quantitatively surveying cell surface markers specifically expressed in undifferentiated embryonic stem cells. These results suggested the value of ZIC‐HILIC as a novel and efficient separation method for comprehensive and quantitative proteomic analyses. Copyright © 2009 John Wiley & Sons, Ltd.     

Low‐molecular‐weight color pI markers to monitor on‐line the peptide focusing process in OFFGEL fractionation

High‐throughput mass spectrometry‐based proteomic analysis requires peptide fractionation to simplify complex biological samples and increase proteome coverage. OFFGEL fractionation technology became a common method to separate peptides or proteins using isoelectric focusing in an immobilized pH gradient. However, the OFFGEL focusing process may be further optimized and controlled in terms of separation time and pI resolution. Here we evaluated OFFGEL technology to separate peptides from different samples in the presence of low‐molecular‐weight (LMW) color pI markers to visualize the focusing process. LMW color pI markers covering a large pH range were added to the peptide mixture before OFFGEL fractionation using a 24‐wells device encompassing the pH range 3–10. We also explored the impact of LMW color pI markers on peptide fractionation labeled previously for iTRAQ. Then, fractionated peptides were separated by RP_HPLC prior to MS analysis using MALDI‐TOF/TOF mass spectrometry in MS and MS/MS modes. Here we report the performance of the peptide focusing process in the presence of LMW color pI markers as on‐line trackers during the OFFGEL process and the possibility to use them as pI controls for peptide focusing. This method improves the workflow for peptide fractionation in a bottom‐up proteomic approach with or without iTRAQ labeling.     

MeCAT peptide labeling for the absolute quantification of proteins by 2D‐LC‐ICP‐MS

Metal‐Coded Affinity Tags (MeCAT) reagents were devised for the absolute quantification of labeled proteins and peptides using inductively coupled plasma mass spectrometry (ICP‐MS). After the recent publication of quantification approaches for digested proteins, this work presents a multidimensional strategy for the application of MeCAT to samples which require higher chromatographic resolution. Two‐dimensional separations based on strong cation exchange (SCX) and reversed‐phase (RP) chromatography, were used for the quantification of lysozyme, bovine serum albumin and transferrin after tryptic digestion. The elution protocols were optimized to improve the resolution of the MeCAT‐labeled peptides which led to faster elutions in SCX and longer retention times in RP compared with unlabeled peptides. The optimized method provided enough resolution for the samples analyzed. Peptides losses during the whole procedure were studied. Although recoveries of greater than 90% were found in the RP dimension, important global losses in the two‐dimensional offline approach forced us to use specific internal standards, in this case MeCAT‐labeled standard peptides. External calibration and label‐specific isotope dilution analysis (IDA) were tested and compared as possible quantification techniques. While both techniques showed accurate and precise determinations, the label‐specific IDA technique resulted in more straightforward measurements and more affordable external calibrations. Finally, simultaneous quantification of three different samples labeled with different lanthanides was successfully performed demonstrating the potential of MeCAT combined with ICP‐MS for multiplexing. Electrospray ionization mass spectrometry techniques provided the structural information needed for the identification of the labeled species. Copyright © 2012 John Wiley & Sons, Ltd.     

The First Zero‐Length Mass Spectrometry‐Cleavable Cross‐Linker for Protein Structure Analysis

Combining the properties of a zero‐length cross‐linker with cleavability by tandem mass spectrometry (MS/MS) poses great advantages for protein structure analysis using the cross‐linking/MS approach. These include a reliable, automated data analysis and the possibility to obtain short‐distance information of protein 3D‐structures. We introduce 1,1′‐carbonyldiimidazole (CDI) as an easy‐to‐use and commercially available, low‐cost reagent that ideally fulfils these features. CDI bridges primary amines and hydroxy groups in proteins with the lowest possible spacer length of one carbonyl unit (ca. 2.6 Å). The cross‐linking reaction can be conducted under physiological conditions in the pH range between 7.2 and 8. Urea and carbamate cross‐linked products are cleaved upon collisional activation during MS/MS experiments generating characteristic product ions, greatly improving the unambiguous identification of cross‐links. Our innovative analytical concept is exemplified and applied for bovine serum albumin (BSA), wild‐type tumor suppressor p53, an intrinsically disordered protein, and retinal guanylyl cyclase activating protein‐2 (GCAP‐2).     

Affinity‐Labeling‐Based Introduction of a Reactive Handle for Natural Protein Modification

A new chemical method to site‐specifically modify natural proteins without the need for genetic manipulation is described. Our strategy involves the affinity‐labeling‐based attachment of a unique reactive handle at the surface of the target protein, and the subsequent selective transformation of the reactive handle by a bioorthogonal reaction to introduce a variety of functional probes into the protein. To demonstrate this approach, we synthesized labeling reagents that contain: 1) a benzenesulfonamide ligand that directs specifically to bovine carbonic anhydrase II (bCA), 2) an electrophilic epoxide group for protein labeling, 3) an exchangeable hydrazone bond linking the ligand and the epoxide group, and 4) an iodophenyl or acetylene handle. By incubating the labeling reagent with bCA, the reactive handle was covalently attached at the surface of bCA through epoxide ring opening. Either after or before removing the ligand by a hydrazone/oxime‐exhange reaction, which restores the enzymatic activity, the reactive handle incorporated could be derivatized by Suzuki coupling or Huisgen cycloaddition reactions. This method is also applicable to the target‐specific multiple modification in a protein mixture. The availability of various (photo)affinity‐labeling reagents and bioorthogonal reactions should extend the flexibility of this strategy for the site‐selective incorporation of many functional molecules into proteins.