Estimating the Efficiency of Phosphopeptide Identification by Tandem Mass Spectrometry
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Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low stoichiometry of phosphorylation and poor phosphopeptide ionization efficiency and fragmentation due to neutral loss. Phosphoproteomics has become an important dimension in systems biology studies, and it is essential to have efficient analytical tools to cover a broad range of signaling events. To evaluate current mass spectrometric performance, we present here a novel method to estimate the efficiency of phosphopeptide identification by tandem mass spectrometry. Phosphopeptides were directly isolated from whole plant cell extracts, dephosphorylated, and then incubated with one of three purified kinases—casein kinase II, mitogen-activated protein kinase 6, and SNF-related protein kinase 2.6—along with 16O4- and 18O4-ATP separately for in vitro kinase reactions. Phosphopeptides were enriched and analyzed by LC-MS. The phosphopeptide identification rate was estimated by comparing phosphopeptides identified by tandem mass spectrometry with phosphopeptide pairs generated by stable isotope labeled kinase reactions. Overall, we found that current high speed and high accuracy mass spectrometers can only identify 20%–40% of total phosphopeptides primarily due to relatively poor fragmentation, additional modifications, and low abundance, highlighting the urgent need for continuous efforts to improve phosphopeptide identification efficiency.
KeywordsProtein phosphorylation Proteomics Tandem mass spectrometry
It is estimated that there are over 500 protein kinases in mammals and over 1000 in plants, and an estimated half or more of all proteins are phosphorylated at certain points during their life span [1, 2]. Reversible phosphorylation of proteins is involved in the regulation of most, if not all, cellular processes . Abnormal phosphorylation has been implicated in a number of diseases, most notably cancer . The accurate determination of sites of phosphorylation and dynamics of this modification in response to extracellular stimulation is important for elucidating complex disease mechanisms and global regulatory networks. Development of methods for analyzing phosphorylated proteins, therefore, has been an active field of research in the signaling, mass spectrometry, and proteomics communities.
Advances in mass spectrometry (MS)-based proteomics have driven increasing efforts to identify reliable approaches for the large scale analysis of phosphoproteins (phosphoproteomics) that include both the identification of protein phosphorylation sites and the quantification of changes in phosphorylation at individual sites . Phosphorylation is often a low stoichiometric event . To identify specific sites of phosphorylation, it is essential to have an efficient strategy for the selective enrichment of actual phosphopeptides. Current approaches include immobilized metal ion or metal oxide affinity chromatography (IMAC and MOAC) [7, 8, 9, 10] and polymer-based metal ion affinity capture (polyMAC) for general phosphopeptide enrichment  and anti-phosphotyrosine antibodies for the isolation of phosphotyrosine-containing peptides . High throughput analysis of phosphorylation using directed enrichment methods followed by MS has become a standard approach for phosphoprotein detection.
While phosphoproteomics has increasingly become an important, typically more informative, dimension in omics studies, its challenges have persisted . The primary challenge in examining protein phosphorylation is its low stoichiometry. Phosphorylated proteins, especially those involved in signaling, are often expressed in relatively low amounts in a cell, and few of these proteins exist in a phosphorylated form at any one time. Furthermore, phosphopeptides have low ionization efficiency due to their negatively charged phosphate groups , and they can exhibit poor fragmentation in tandem mass spectra because of neutral loss of the phosphate groups . Finally, informatics approaches for processing the results of mass spectrometry data for phosphopeptides are not yet mature .
There have been a number of attempts to improve phosphopeptide identification efficiency, particularly by alternative activation methods . Faster and more accurate LC-MS systems have also made a significant contribution toward enhancing the coverage of the phosphoproteome, but it is not still clear what percentage of the phosphopeptide population is routinely identified by tandem mass spectrometry (MS/MS) and whether current phosphoproteomic strategies provide true representations of the phosphoproteome for systems biology analyses. Due to the dynamic nature of phosphorylation, low coverage of the phosphoproteome at certain cellular states might lead to biased or even incorrect conclusions. Here, we present a novel strategy to estimate the efficiency of phosphopeptide identification by tandem mass spectrometry. Instead of using a large pool of synthetic phosphopeptides, which is costly to generate  and still incomprehensive, we created a phosphopeptide pool directly from whole cell extracts. To generate phosphopeptides with distinctively recognizable features in the mass spectra, we introduced in vitro kinase reactions with 16O4- and 18O4-ATP to generate phosphopeptide pairs with similar intensity that are separated by 6 Da on mass spectra. Previous literature and our own data indicate that the 18O atoms on the γ-phosphoryl group do not exchange with water during kinase reactions . Thus, the efficiency of phosphopeptide identification can be estimated by comparing the phosphopeptides identified by MS/MS with the total number of phosphopeptide pairs that demonstrate the distinctive mass shift.
Plant Materials and Growth
The seeds of Col-0 wild type Arabidopsis were geminated on half-strength Murashige and Skoog (MS) medium (1% sucrose with 0.6% phytogel). Five d after germination, seedlings were transferred into 40 mL half-strength MS liquid medium with 1% sucrose at 22 °C in continuous light on a rotary shaker set at 100 rpm. For osmotic stress treatment, 12-d-old seedlings were transferred into fresh medium containing 800 mM Mannitol for 30 min. In parallel, the seedlings transferred into fresh medium were used as the control.
Protein Extraction and Digestion
Plant tissues were ground with mortar and pestle in liquid nitrogen, and the ground tissues were lysed in 6 M guanidine hydrochloride containing 100 mM Tris-HCl (pH = 8.5) with EDTA-free protease inhibitor cocktail (Roche, Madison, WI, USA) and phosphatase inhibitor cocktail (Sigma-Aldrich, St. Louis, MO, USA). Proteins were reduced and alkylated with 10 mM tris-(2-carboxyethyl)phosphine (TECP) and 40 mM chloroacetamide (CAA) at 95 °C for 5 min. Alkylated proteins were subjected to methanol-chloroform precipitation, and precipitated protein pellets were solubilized in 8 M urea containing 50 mM triethylammonium bicarbonate (TEAB). Protein amount was quantified by BCA assay (Thermo Fisher Scientific, Rockford, IL, USA). Protein extracts were diluted to 4 M urea and digested with Lys-C (Wako, Osaka, Japan) in a 1:100 (w/w) enzyme-to-protein ratio overnight at 37 °C. Digests were acidified with 10% trifluoroacetic acid (TFA) to a pH ~2 and desalted using a 100 mg Sep-Pak C18 column (Waters, Milford, MA, USA).
Stable Isotope Labeled In Vitro Kinase Reaction
The in vitro kinase reaction was performed based on previous reports [20, 21] with some modifications. The Lys-C digested peptides (200 μg) were treated with a thermosensitive alkaline phosphatase (TSAP) (Roche) in a 1:100 (w/w) enzyme-to-peptide ratio at 37 °C overnight for dephosphorylation, and the dephosphorylated peptides were desalted using Sep-Pak C18 column. The desalted peptides were resuspended in kinase reaction buffer (50 mM Tris-HCl, 10 mM MgCl2, and 1 mM DTT, pH 7.5) with either 1 mM 16O-ATP or γ-[18O4]-ATP (Cambridge Isotope Laboratories, MA, USA). The suspended peptides were incubated with the recombinant SNF-related protein kinase 2.6 (SnRK2.6), mitogen-activated protein kinase 6 (MPK6), or casein kinase II (CK2) (500 ng) at 30 °C overnight. The kinase reaction was quenched by acidifying with 10% TFA to a final concentration of 1%, and the peptides were desalted by Sep-Pak C18 column. The light and heavy phosphopeptides were mixed and further digested by trypsin at 37 °C for 6 h. Tryptic phosphopeptides were desalted by Sep-Pak column, and then were enriched by PolyMAC-Ti reagent, and the eluates were dried in a SpeedVac for LC-MS/MS analysis.
Phosphopeptide enrichment was performed according to the reported PolyMAC-Ti protocol  with some modifications. Tryptic peptides (200 μg) were resuspended in 100 μL of loading buffer [80% acetonitrile (ACN) with 1% TFA] and incubated with 25 μL of the PolyMAC-Ti reagent for 20 min. A magnetic rack was used to collect the magnetic beads to the sides of the tubes, and the flow-through was discarded. The magnetic beads were washed with 200 μL of washing buffer 1 (80% ACN, 0.2% TFA with 25 mM glycolic acid) for 5 min, and washing buffer 2 (80% ACN in water) for 30 s. Phosphopeptides were then eluted with 200 μL of 400 mM NH4OH with 50% ACN and dried in a SpeedVac.
The phosphopeptides were dissolved in 5 μL of 0.3% formic acid (FA) with 3% ACN and injected into an Easy-nLC 1000 (Thermo Fisher Scientific). Peptides were separated on a 45 cm in-house packed column (360 μm o.d. × 75 μm i.d.) containing C18 resin (2.2 μm, 100Å; Michrom Bioresources, Auburn, CA) with a 30 cm column heater (Analytical Sales and Services, Pompton Plains, NJ) set at 50 °C. The mobile phase buffer consisted of 0.1% FA in ultra-pure water (buffer A) with an eluting buffer of 0.1% FA in 80% ACN (buffer B) run over a linear 60 min gradient of 5%–30% buffer B at a flow rate of 250 nL/min. The Easy-nLC 1000 was coupled online with a LTQ-Orbitrap Velos Pro mass spectrometer (Thermo Fisher Scientific). The mass spectrometer was operated in the data-dependent mode in which a full MS scan (from m/z 350–1500 with the resolution of 30,000 at m/z 400) was followed by the five most intense ions being subjected to collision-induced dissociation (CID) fragmentation. CID fragmentation was performed and acquired in the linear ion trap (normalized collision energy (NCE) 30%, AGC 3e4, max injection time 100 ms, isolation window 3 m/z, and dynamic exclusion 60 s).
The raw files were searched directly against the Arabidopsis thaliana database (TAIR10) with no redundant entries using MaxQuant software (ver. 126.96.36.199)  with the Andromeda search engine. Initial precursor mass tolerance was set at 20 ppm, the final tolerance was set at 6 ppm, and the ITMS MS/MS tolerance was set at 0.6 Da. Search criteria included a static carbamidomethylation of cysteines (+57.0214 Da) and variable modifications of (1) oxidation (+15.9949 Da) on methionine residues, (2) acetylation (+42.011 Da) at the N-terminus of proteins, (3) phosphorylation (+79.996 Da), and (4) heavy phosphorylation (+85.979 Da) on serine, threonine, or tyrosine residues. The match between runs function was enabled with 1.0 min match time window. The searches were performed with trypsin digestion and allowed a maximum of two missed cleavages on the peptides analyzed from the sequence database. The false discovery rates for proteins, peptides, and phosphosites were set at 0.01. The minimum peptide length was six amino acids, and a minimum Andromeda score cut-off was set at 40 for modified peptides. A site localization probability of 0.75 was used as the cut-off for localization of phosphorylation sites. The MS/MS spectra can be viewed through the MaxQuant viewer. For the ProteomeDiscoverer searches, the raw files were searched directly against the same Arabidopsis thaliana database (TAIR10) with no redundant entries using the SEQUEST HT algorithm in Proteome Discoverer ver. 2.1 (Thermo Fisher Scientific). Peptide precursor mass tolerance was set at 10 ppm, and MS/MS tolerance was set at 0.6 Da. Search criteria included a static carbamidomethylation of cysteines (+57.0214 Da) and variable modifications of (1) oxidation (+15.9949 Da) on methionine residues, (2) acetylation (+42.011 Da) on protein N-termini, (3) phosphorylation (+79.996 Da), and (4) heavy phosphorylation (+85.979 Da) on serine, threonine, or tyrosine residues. Searches were performed with full tryptic digestion and allowed a maximum of two missed cleavages on the peptides analyzed from the sequence database. Relaxed and strict false discovery rates (FDR) were set to 0.05 and 0.01, respectively. All localized phosphorylation sites were submitted to Motif-X  to determine kinase phosphorylation motifs with the TAIR10 database as the background. The significance was set at 0.000001, the width was set at 13, and the number of occurrences was set at 20. The light and heavy phosphopeptide and peak pairs were identified through the LAXIC algorithm . All of the light and heavy phosphopeptide and peak pairs are listed in the Supplementary Tables, and the raw data and analysis files for the proteomic analyses have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the jPOST partner repository (http://jpost.org)  with the data set identifier PXD005079.
Results and Discussion
We generated whole cell lysates from Arabidopsis seedlings in this study. The plant has over 1000 encoded kinases, and whole cell lysates likely contain tens of thousands of phosphorylation sites [2, 26]. Two plant kinases, MAPK6 and SnRK2.6, were recombinantly expressed and purified. Along with human recombinant CK2, the three kinases were incubated with Arabidopsis lysate and γ-16O4- or γ-18O4-ATP separately. Each kinase reaction can generate hundreds of phosphopeptides, which is sufficient for this study but still well within the capacity of a typical high resolution LC-MS system today. This strategy also minimizes the instrumentation factor. Although it is conceivable that the speed of mass spectrometers affects the identification rate of phosphopeptides, this factor would be minor with the current approach.
Number of Phosphopeptide Pairs in MS Spectra and Phosphopeptides Identified by MS2. MQ is MaxQuant and PD is Proteome Discover
We also examined the effect of different search algorithms. Besides MaxQuant, we also searched the MS/MS spectra using Proteome Discoverer 2.1. MaxQuant is based on Andromeda whereas Proteome Discoverer uses Sequest HT as the search engine. Overall, with the same FDR cutoff value (FDR <1%), there are some obvious difference in the number of phosphopeptides identified by Andromeda (MaxQuant) or Sequest HT (Proteome Discoverer), but the efficiency of phosphopeptide identification is within a similar range (Table 1 and Figure 4).
Large scale analysis of protein phosphorylation, or phosphoproteomics, has become an important component of systems biology studies. While the advances of mass spectrometers in speed and accuracy, along with the introduction of ultra-high performance liquid chromatography, have greatly improved phosphoproteome coverage, it is critical to evaluate whether the phosphoproteomic data is comprehensive, especially considering that protein phosphorylation is highly dynamic. We have presented a novel method to estimate the efficiency of phosphopeptide identification by generating a large pool of phosphopeptides through direct isolation from cell lysates and in vitro kinase reactions. These phosphopeptides can be recognized according to specific features, though they may or may not be isolated for MS/MS. Examination of MS/MS data and MS features indicates that, on average, 30% of phosphopeptides were identified by MS/MS. Poor fragmentation and low abundance contribute to 70% of the phosphopeptides not being identified by MS/MS. This study highlights the need for additional efforts to increase the yield of phosphopeptides for MS analyses, possibly through better sample preparation, phosphopeptide enrichment, and LC resolution, and to further improve phosphopeptide fragmentation through alternative methods.
This study was partially supported by NIH grants 1R01GM111788 and 5R01GM088317, and NSF grant 1506752.
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