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Post-translational modifications (PTMs) change protein structures and functions. Methods for the simultaneous enrichment of multiple PTM types can maximize coverage in analyses. We present a protocol using dual-functional Ti(IV)-immobilized metal affinity chromatography followed by mass spectrometry for the simultaneous enrichment and analysis of protein N-glycosylation and phosphorylation in pancreatic tissues.
Mass spectrometry can provide deep coverage of post-translational modifications (PTMs), although enrichment of these modifications from complex biological matrices is often necessary due to their low stoichiometry in comparison to non-modified analytes. Most enrichment workflows of PTMs on peptides in bottom-up proteomics workflows, where proteins are enzymatically digested before the resulting peptides are analyzed, only enrich one type of modification. It is the entire complement of PTMs, however, that leads to biological functions, and enrichment of a single type of PTM may miss such crosstalk of PTMs. PTM crosstalk has been observed between protein glycosylation and phosphorylation, the two most common PTMs in human proteins and also the two most studied PTMs using mass spectrometry workflows. Using the simultaneous enrichment strategy described herein, both PTMs are enriched from post-mortem human pancreatic tissue, a complex biological matrix. Dual-functional Ti(IV)-immobilized metal affinity chromatography is used to separate various forms of glycosylation and phosphorylation simultaneously in multiple fractions in a convenient spin tip-based method, allowing downstream analyses of potential PTM crosstalk interactions. This enrichment workflow for glyco- and phosphopeptides can be applied to various sample types to achieve deep profiling of multiple PTMs and identify potential target molecules for future studies.
Protein post-translational modifications (PTMs) play a major role in modulating protein structures and consequently their functions and downstream biological processes. The diversity of the human proteome increases exponentially due to the combinatorial variability afforded by various PTMs. Different variants of proteins from their canonical sequences as predicted by the genome are known as proteoforms, and many proteoforms arise from PTMs1. Studying proteoform diversity in health and disease has become an area of research of great interest in recent years2,3.
The study of proteoforms and more specifically PTMs with great depth has become more facile through the development of mass spectrometry (MS)-based proteomics methods. Using MS, analytes are ionized, fragmented, and identified based on the m/z of fragments. Enrichment methods are often necessary due to the low relative abundance of PTMs compared to non-modified forms of proteins. Though analysis of intact proteins and their PTMs, called top-down analyses, have become more routine, the enzymatic digestion of proteins and the analysis of their component peptides in bottom-up analyses is still the most widely used route for PTM analysis. The two most widely studied PTMs, and the two most common PTMs in vivo, are glycosylation and phosphorylation4. These two PTMs play major roles in cell signaling and recognition and thus are important modifications to characterize in disease research.
The chemical properties of various PTMs often provides routes toward enrichment of these PTMs at the protein and peptide levels prior to analysis. Glycosylation is a hydrophilic PTM due to the abundance of hydroxyl groups on each monosaccharide. This property can be used to enrich glycopeptides in hydrophilic interaction chromatography (HILIC), which can separate more hydrophilic glycopeptides from the hydrophobic non-modified peptides5. Phosphorylation adds the phosphate moiety, which is negatively charged except at acidic pH. Due to this charge, various metal cations, including titanium, can be used to attract and bind phosphopeptides while non-phosphorylated species are washed away. This is the principle of immobilized metal affinity chromatography (IMAC). Further discussions of these and other enrichment strategies for glycosylation and phosphorylation can be found in recent reviews6,7.
Comparatively large amounts of starting peptide material (0.5 mg or more) are often needed for enrichment protocols due to the low stoichiometry of PTMs on peptides. In scenarios where this amount of sample may not be easily obtained, such as tumor core biopsy or cerebrospinal fluid analyses, it is beneficial to use facile workflows that result in maximum biomolecular information. Recent strategies developed by our lab and others have highlighted the simultaneous and parallel analysis of glycosylation and phosphorylation using the same PTM enrichment workflow8,9,10,11,12. Though the chemical properties of these two PTMs may differ, these PTMs may be analyzed in multiple steps due to the innovative separation techniques and materials used. For example, electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) overlays separations based on hydrophilic interactions between analytes and the mobile phase with charge-charge interactions between analytes and the stationary phase material13,14,15,16. At acidic pH, the attraction of phosphorylated peptides to the stationary phase can improve their retention and separation from non-modified peptides. Material consisting of Ti(IV) immobilized on hydrophilic microspheres can be used for HILIC and IMAC-based elution to separate phosphopeptides and neutral, acidic, and mannose-6-phosphorylated glycopeptides17,18. This strategy is known as dual-functional Ti(IV)-IMAC. Using these strategies for enriching multiple PTMs in a single workflow can make analyses of potential PTM crosstalk interactions more accessible. Additionally, the total sample amount and time requirements are less than the conventional enrichment methods when performed in parallel (i.e., HILIC and IMAC on separate sample aliquots).
To demonstrate the dual-functional Ti(IV)-IMAC strategy for simultaneous analysis of protein glycosylation and phosphorylation, we have applied it to analyze post-mortem human pancreatic tissues. The pancreas produces both digestive enzymes and regulatory hormones, including insulin and glucagon. The pancreatic function is impaired in pancreatic disease. In diabetes, the regulation of blood sugar is affected, leading to higher levels of glucose in the blood. In pancreatitis, inflammation results from auto-digestion of the organ3. Changes in PTM profiles, including glycosylation and phosphorylation, may result, as is often the case, in other diseases.
Here, we describe a protocol for a spin-tip based simultaneous enrichment method, based on a dual-functional Ti(IV)-IMAC strategy, for N-glycopeptides and phosphopeptides derived from proteins extracted from pancreatic tissue. The protocol includes protein extraction and digestion, enrichment, MS data collection, and data processing, as can be seen in Figure 1. Representative data from this study are available via ProteomeXchange Consortium with identifier PXD033065.
Figure 1: Workflow for simultaneous analysis of N-glycopeptides and phosphopeptides from human pancreatic tissues. Tissues are first cryo-pulverized into a fine powder before protein extraction using the detergent sodium dodecyl sulfate (SDS). Proteins are then subjected to enzymatic digestion. The resulting peptides are aliquoted prior to enrichment using dual-functional Ti(IV)-IMAC. Raw data is collected using nanoscale reversed phase liquid chromatography-mass spectrometry (nRPLC-MS) and is analyzed using database searching software. Please click here to view a larger version of this figure.
This protocol is intended to make PTM analyses more accessible and to enable more widespread analysis of multiple PTMs in the same workflow. This protocol can be applied to other complex biological matrices, including cells and biofluids.
Consent was obtained for the use of pancreatic tissues for research from the deceased's next of kin and an authorization by the University of Wisconsin-Madison Health Sciences Institutional Review Board was obtained. IRB oversight is not required because it does not involve human subjects as recognized by 45 CFR 46.102(f).
CAUTION: Care should be taken when handling the reagents used in this protocol, which include acids (formic, acetic, trifluoroacetic), bases (ammonium hydroxide), and cryogens (liquid nitrogen). Read the safety data sheets for the reagents used to become familiar with the associated hazards and needed precautions. Concentrations denoted using percentages are volume/total volume (v/v) and are diluted with water.
1. Tissue cryo-pulverization, lysis, and protein extraction
2. Protein digestion and desalting
3. ERLIC N-glycopeptide enrichment
NOTE: Exact centrifuge speeds and times may differ based on samples and must be optimized. In general, 300 x g for 2 min is appropriate for conditioning and washing of the material and 100 x g for 5 min for eluting.
4. Ti(IV)-IMAC phosphopeptide enrichment
NOTE: Exact centrifuge speeds and times may differ based on samples and must be optimized. In general, 300 x g for 2 min is appropriate for conditioning and washing of the material and 100 x g for 5 min for eluting.
5. Dual-functional Ti(IV) simultaneous enrichment
NOTE: Exact centrifuge speeds and times may differ based on samples and must be optimized. In general, 300 x g for 2 min is appropriate for conditioning and washing of the material and 100 x g for 5 min for eluting.
6. Nano-flow reversed phase liquid chromatography-mass spectrometry (nRPLC-MS)
NOTE: MS data acquisition and analysis methods are diverse, and thus only one suggested LC-MS pipeline (and its associated parameters) is described here in the following steps. Samples generated using the previously outlined sample preparation and enrichment steps can be analyzed using other instrumental set-ups, including using commercially available chromatographic columns, given sufficient data quality.
7. MS data analysis
NOTE: One data analysis pipeline using two different software to analyze the same dataset is presented here. Phosphorylation and glycosylation can be searched at the same time using a single software instead of two separate software as described here, though in general, software search time is proportional to the search space, i.e., number of PTMs considered. For this reason, two different software are used in parallel to the search for glycopeptides and phosphopeptides.
Representative mass spectrometry data, including raw files and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD03306522.
In this work, duplicate injection replicates were analyzed for each enrichment elution. Identifications made from both technical replicates were collated in the final analysis. Due to the semi-stochastic nature of data-dependent acquisition in picking peptid...
The dual-functional Ti(IV)-IMAC strategy is useful for the simultaneous analysis of N-glycopeptides and phosphopeptides from the same sample in a single sample preparation workflow. ERLIC-based methods have also been shown to perform simultaneous enrichment of PTMs. Both strategies have been used previously for deep coverage in PTM analyses14,18. In adapting the dual Ti method to decreasing sample incubation time by using spin-tips, we hope that this protocol has...
The authors declare no competing interests.
This research was supported in part by grant funding from the NIH (R01DK071801, RF1AG052324, P01CA250972, and R21AG065728), and Juvenile Diabetes Research Foundation (1-PNF-2016-250-S-B and SRA-2016-168-S-B). Data presented here were also in part obtained through support from an NIH/NCATS UL1TR002373 award through the University of Wisconsin Institute for Clinical and Translational Research. The Orbitrap instruments were purchased through the support of an NIH shared instrument grant (NIH-NCRR S10RR029531) and Office of the Vice Chancellor for Research and Graduate Education at the University of Wisconsin-Madison. We would also like to acknowledge the generous support of the University of Wisconsin Organ and Tissue Donation Organization who provided human pancreas for research and the help of Dan Tremmel, Dr. Sara D. Sackett, and Prof. Jon Odorico for providing the samples to our lab. Our research team would like to give special thanks to the families who donated tissues for this study. L.L. acknowledges NIH grant S10OD025084, a Pancreas Cancer Pilot grant from the University of Wisconsin Carbone Cancer Center (233-AAI9632), as well as a Vilas Distinguished Achievement Professorship and the Charles Melbourne Johnson Distinguished Chair Professorship with funding provided by the Wisconsin Alumni Research Foundation and University of Wisconsin-Madison School of Pharmacy.
Name | Company | Catalog Number | Comments |
Acetic Acid, Glacial (Certified ACS) | Fisher Scientific | A38S-500 | |
Acetone (Certified ACS) | Fisher Scientific | A18-1 | |
Acetonitrile, Optima LC/MS Grade | Fisher Scientific | A955-4 | |
Ammonium Acetate (Crystalline/Certified ACS) | Fisher Scientific | A637-500 | |
Ammonium Hydroxide (Certified ACS Plus) | Fisher Scientific | A669-212 | |
Byonic software | Protein Metrics | n/a | Commercial software used for glycoproteomic analysis (https://proteinmetrics.com/byos/) |
C18 BEH material | Waters | 186002353 | Material removed from column and used to pack nano capillaries (pulledto integrate tip used directly in line with instrument inlet) |
CAE-Ti-IMAC, 100% | J&K Scientific | 2749380-1G | Material used for dual-functional Ti(IV)-IMAC; can also be used for conventional IMAC/conventional phosphopeptide enrichment |
Cellcrusher kit | Cellcrusher | n/a | Used for grinding tissue samples into powder before extraction |
Eppendorf 5424R Microcentrifuge | Fisher Scientific | 05-401-205 | For temperature-controlled centrifugation |
cOmplete protease inhibitor cocktail tablets | Sigma | 11697498001 | |
DTT, Molecular Grade (DL-Dithiothreitol) | Promega | V3151 | Protein reducing agent |
Ethanol, 200 proof (100%), USP | Fisher | 22-032-601 | |
Fisherbrand Analog Vortex Mixer | Fisher Scientific | 02-215-414 | |
Fisherbrand Low-Retention Microcentrifuge Tubes (1.5 mL) | Fisher Scientific | 02-681-320 | |
Fisherbrand Low-Retention Microcentrifuge Tubes (2 mL) | Fisher Scientific | 02-681-321 | |
Fisherbrand Model 120 Sonic Dismembrator | Fisher Scientific | FB120110 | For sample lysis using ultrasonication |
Formic Acid, 99.0+%, Optima LC/MS Grade | Fisher Scientific | A117-50 | |
Fused silica capillary (75 μm inner diameter, 360 μm outer diameter) | Polymicro Technologies LLC | 100 m TSP075375 | For in-house pulled and packed columns with integrated emitter |
Hydrofluoric acid (48 wt. % in H2O) | Sigma-Aldrich | 339261-100ML | Used for opening emitter of pulled capillary column |
Iodoacetamide, BioUltra | Sigma | I1149-5G | Protein reducing reagent |
MaxQuant software | n/a | n/a | Free software used for phosphoproteomic analysis (https://www.maxquant.org/) |
Multi-therm Shaker with heating and cooling | Benchmark Scientific | H5000-HC | Heating block |
Oasis HLB 1 cc Vac Cartridge, 10 mg Sorbent per Cartridge, 30 µm, 100/pk | Waters | 186000383 | Larger-scale cartridge desalting for tryptic digests (loading capacity approximately up to 1 mg each) |
OMIX C18 pipette tips, 100 µL tip, 10 - 100 μL elution volume, 1 x 96 tips | Agilent | A57003100 | Smaller-scale packed pipette tip for desalting for enrichment elutions |
P-2000 Micropipette Puller | Sutter Instrument Co. | P-2000/F | For pulling nano-capillary columns for LC-MS |
PhosSTOP phosphatase inhibitor tablets | Sigma | 4906845001 | |
Pierce BCA Protein Assay Kit | Thermo Fisher Scientific | 23225 | |
Pierce Quantitative Colorimetric Peptide Assay | Thermo Fisher Scientific | 23275 | |
PolySAX LP (12 μm, pore size 300 Å) | PolyLC | BMSX1203 | Material for strong anion-exchange chromatography used for ERLIC/conventional glycopeptide enrichment |
Potassium Phosphate Monobasic (Crystalline/Certified ACS) | Fisher Scientific | P285-500 | |
Pressure injection cell with integrated magnetic stirplate | Next Advance | PC77-MAG | For packing nano-capillary columns with stationary phase up to 2500 psi limit |
Proteome Discoverer software | Thermo Fisher Scientific | n/a | Commercial software for proteomics anaysis (with integrated database searching software nodes) and data visualization (https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html) |
SpeedVac SC110 Vacuum Concentrator Model SC110-120 | Savant | n/a | Centrifugal vacuum concentrator for drying samples (under heat) |
SDS Solution, 10% Sodium Dodecyl Sulfate Solution, Molecular Biology/Electrophoresis | Fisher Scientific | BP2436200 | |
Sequencing Grade Modified Trypsin | Promega | V5111 | |
Sodium Chloride (Crystalline/Certified ACS) | Fisher Scientific | S271-500 | |
TopTip, Empty, 10-200 µL, Pack of 96 | Glygen Corporation | TT2EMT.96 | Empty pipette tip with micron-sized hole used that can be used to pack chromatographic materials for enrichments, bundled with tube adapters |
Triethylammonium bicarbonate buffer (TEAB, 1 M, pH 8.5 (volatile)) | Sigma | 90360-100ML | |
Trifluoroacetic acid, Reagent Grade, 99% | Fisher Scientific | 60-017-61 | |
Tris Base (White Crystals or Crystalline Powder/Molecular Biology) | Fisher Scientific | BP152-500 | |
Trypsin/Lys-C Mix, Mass Spec Grade | Promega | V5071 | |
Urea (Certified ACS) | Fisher Scientific | U15-500 | |
Water, Optima LC/MS Grade | Fisher Scientific | W64 |
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