This work was supported by the grant P01HL107151 from the NHLBI/NIH. The authors also gratefully acknowledge the support and access to instrumentation provided through grant P41GM103490 from the NIGMS/NIH.

NOTE: Lab Safety Concerns
In keeping with standard laboratory best practices, observe the following. Store all organic solvents in appropriate locations. Keep all waste materials in chemical waste containers with clear labeling of chemical compositions. As several reagents used in these protocols are potential carcinogens or generate volatile combustible gases, handle all reagents in a fume hood with ventilation. Wear personal protective equipment such as gloves, lab coat, and...

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The authors declare no competing financial interest.

Combining in-gel reductive &#946;-elimination with aqueous-organic extraction enhances the sensitivity and depth of structural data that can be acquired for characterizing sulfated and non-sulfated O-linked glycans harvested from small amounts of mucin-type glycoproteins resolved from other proteins by SDS-PAGE. The essential advances of the technical approaches presented in this study are: (a) facile removal of gel derived contaminants by simple washing steps; (b) quantitative recovery of permethylated sulfoglycans in t...

Glycosylation is an essential protein post-translational modification, contributing to organismal physiology, tissue pathology, and cellular recognition 1-3. Despite major advances in analytical glycoscience, characterizing the complete diversity of glycans on a specific protein remains an extremely challenging task, especially on proteins isolated from primary biological sources. Nonetheless, the microheterogeneity of glycoprotein glycans frequently affects functional interactions with other proteins. Therefore, characterization of glycan diversity is essential for understanding the physiological significance of cellular and tissue glycosylation 4,5. In order to understand the contribution of glycoprotein glycosylation to tissue physiology and pathophysiology, robust, sensitive, and comprehensive glycomic analytical techniques have become increasingly important. In proteomic analysis, protein identifications are generally achieved by LC-MS/MS analysis of tryptic peptides 6. Protein digestion can be carried out using a purified protein or proteins resolved by SDS-PAGE following in-gel digestion with proteases such as trypsin 7-9. Pre-enrichment of the protein mixture by SDS-PAGE enhances the depth and accuracy of protein ID. The development of analogous strategies for glycomic analysis of glycoprotein glycosylation lies at the forefront of glycoscience.
The two major classes of glycans are attached to protein backbones through either N-linkage or O-linkage. N-linked glycans are attached to asparagine (Asn) residues found as part of a sequon defined as Asn-X-Ser/Thr/Cys (X is any amino acid except proline), and can be released by enzymatic digestion with peptide-N-glycanase (PNGaseF or A), either in solution, in-gel, or on-blot 10-12. O-linked glycans are mainly attached to serine (Ser) or threonine (Thr) residues. However, only one enzyme has been identified that is capable of releasing O-linked glycans from glycoprotein and it has an extremely limited glycan specificity, releasing only the simplest O-linked glycans. Chemical release strategies remain the method of choice for comprehensive release of O-linked glycans from glycoproteins. Reductive or non-reductive &#946;-elimination, or hydrazinolysis are well-characterized chemical release techniques and are currently the most commonly used approaches for releasing O-linked glycans from glycoproteins 13,14. Although reductive &#946;-elimination has been used to release O-linked glycans from glycoproteins separated by SDS-PAGE, previous approaches required HPLC separation for subsequent analysis 15-17.
Multidimensional MS (MSn) analysis currently provides the richest source of structural data for characterizing glycans released from glycoproteins isolated in the amounts expected from most biological sources. The depth of MS-based structural characterization is greatly facilitated by permethylating the released glycans prior to their analysis. Permethylation enhances ionization and tends to equalize molar signal responses across a broad range of glycan structures 18,19. In addition, permethylation unambiguously tags terminal and substituted monosaccharide moieties with distinctive masses, thereby enhancing structural elucidation 20-23. For example, acidic glycans are generally difficult to detect as non-permethylated species by MS. Although acidic glycans can be detected in negative ion mode by MS, it is impossible to detect both acidic and neutral glycans in the same ion mode. A major advantage of glycan permethylation is that all of the free hydroxyl groups (OH) on a glycan&#8217;s monosaccharide substituents will be capped with a methyl group (OCH3 or OMe), thus a sialylated glycan&#8217;s charges are neutralized, making them as detectable as permethylated neutral (asialo) glycans. However, the hydroxyls of sulfate moieties on sulfoglycans are resistant to permethylation, resulting in retention of anionic charge, which suppresses ionization and decreases sensitivity. This suppression currently prevents comprehensive glycomic analysis of very complex glycoproteins such as mucins, which carry a high abundance of sulfated glycans 24-26.
Recent reports on purifying sulfated glycans used charged, reverse-phase chromatography to purify and separate permethylated glycans prior to MALDI analysis. This method relies on complete separation of sulfated and non-sulfated glycans using different mobile phases for elution, which we have found to be less stringent than organic phase partitioning. Therefore, new techniques suitable for the detection and enrichment of sulfoglycans are presented here. These techniques allow for the quantitative recovery of sulfated glycans in the aqueous phase following water:DCM (dichloromethane) extraction, which is routinely performed at the end of glycan permethylation reactions 27. Importantly, this robust separation of permethylated sulfoglycans from a mixture of permethylated non-sulfated glycans concomitantly enriches for charged species while also simplifying MS2 fragmentation patterns. A comprehensive protocol for improved in-gel O-linked glycan analysis is also presented. The improved protocol enhances glycan recovery, increases the structural information obtainable through MSn analysis of permethylated glycans, and improves the sensitivity of sulfoglycomic analyses applied to essential glycoproteins isolated from biological sources.
This protocol is intended for O-linked glycan analysis of whole glycoprotein extracts or of a specific glycoprotein of interest resolved by SDS-PAGE and is composed of three experimental procedures; A) gel clean-up, B) in-gel reductive &#946;-elimination, and C) glycan permethylation. The goal is to obtain comprehensive O-linked glycomic data for glycoproteins harvested from primary sources of biological interest (Figure 1). Glycoproteins separated by SDS-PAGE are visualized by staining and bands of interest are excised and the resulting gel band is sliced into small pieces. The gel pieces are destained and subjected to ethyl acetate washes to remove gel contaminants (Figure 2A). Glycan release is achieved by in-gel reductive &#946;-elimination (Figure 2B) and the released glycans are permethylated. Aqueous-organic extraction following permethylation quantitatively partitions the anionic sulfated glycans away from non-sulfated neutral glycans (Figure 2C). In-gel reductive &#946;-elimination coupled to aqueous-organic extraction enables the characterization of O-linked glycans and sulfoglycans released from small amounts of glycoprotein separated by SDS-PAGE. The strategic overview is summarized in Figure 1 and the details are shown in Figure 2. In addition, a portion of the destained and washed gel pieces can be used for protein ID by standard LC-MS/MS proteomic techniques.

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		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Name of Material/ Equipment</td>
			<td style="width:155px;">Company</td>
			<td style="width:124px;">Catalog Number</td>
			<td style="width:303px;">Comments/Description</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;width:231px;">Water, deionized water</td>
			<td style="width:155px;">Sigma-Aldrich&#160;</td>
			<td>270733-4L</td>
			<td style="width:303px;">CHROMASOLV, for HPLC</td>
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		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Acetic acid, Glacial</td>
			<td style="width:155px;">Fisher</td>
			<td>A38-500</td>
			<td style="width:303px;">Certified ACS&#8805;99.7 w/w %</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Methanol</td>
			<td style="width:155px;">Sigma-Aldrich&#160;</td>
			<td>34860-4L-R</td>
			<td style="width:303px;">CHROMASOLV, for HPLC, &#8805;99.9%</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Ammonium bicarbonate</td>
			<td style="width:155px;">Fluka</td>
			<td>09830-500G</td>
			<td style="width:303px;">BioUltra, &#8805;99.5% (T), Step 1</td>
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		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Acetonitrile</td>
			<td style="width:155px;">Sigma-Aldrich&#160;</td>
			<td>34998-4L</td>
			<td style="width:303px;">CHROMASOLV Plus, for HPLC, &#8805;99.9%, Step 1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Ethyl acetate</td>
			<td style="width:155px;">Fluka</td>
			<td>34972-1L-R</td>
			<td style="width:303px;">LC-MS CHROMASOLV, Step 1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Sodium borohydride</td>
			<td style="width:155px;">Aldrich</td>
			<td>213462-25G</td>
			<td style="width:303px;">ReagentPlus, 99%, Step 2</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Iodomethane</td>
			<td style="width:155px;">Sigma-Aldrich&#160;</td>
			<td>289566-100G</td>
			<td style="width:303px;">ReagentPlus, 99.5%,&#160; Step 6.&#160; Store at 4 &#176;C until use.&#160; Sit at room temperature before use.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Sodium hydroxide solution, 50% w/w</td>
			<td style="width:155px;">Fisher</td>
			<td>SS254-1</td>
			<td style="width:303px;">Certified, Step 6</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Dimethyl sulfoxide, anhydrous</td>
			<td style="width:155px;">Sigma-Aldrich&#160;</td>
			<td>276855-1L</td>
			<td style="width:303px;">Anhydrous, &#8805;99.9%, Step 6</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Methanol, anhydrous</td>
			<td style="width:155px;">Sigma-Aldrich&#160;</td>
			<td>322415-100ML</td>
			<td style="width:303px;">Anhydrous, 99.8%, Step 6</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Dichloromethane</td>
			<td style="width:155px;">Sigma-Aldrich&#160;</td>
			<td>34856-4L</td>
			<td style="width:303px;">CHROMASOL&#174;, for HPLC, &#8805;99.8%, contains amylene as stabilizer, Step 7</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:231px;">Dowex 50WX8 hydrogen formhydrogen form 100-200&#160;mesh</td>
			<td style="width:155px;">Sigma-Aldrich&#160;</td>
			<td>217506-500G</td>
			<td style="width:303px;">Step 3</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">AG 50W-X8 Resin&#160;</td>
			<td style="width:155px;">Bio-Rad</td>
			<td>142-1441</td>
			<td style="width:303px;">Step 3</td>
		</tr>
		<tr height="23">
			<td height="23" style="height:23px;width:231px;">BAKERBOND spe 1 ml x 100 mg Solid Phase Extraction Column, PP, Octadecyl (C18) Reverse Phase</td>
			<td style="width:155px;">JT Baker</td>
			<td>JT-7020-01</td>
			<td style="width:303px;">Step 5 and 8</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">7.5% Mini-PROTEAN TGX Precast Gel&#160;</td>
			<td style="width:155px;">Bio-Rad</td>
			<td></td>
			<td style="width:303px;">Step 1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Bio-Safe Coomassie Stain&#160;</td>
			<td style="width:155px;">Bio-Rad</td>
			<td>161-0786</td>
			<td style="width:303px;">G-250, Step 1</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Silver Stain Kit for Mass Spectrometry</td>
			<td style="width:155px;">Pierce</td>
			<td>24600</td>
			<td style="width:303px;">Step 1</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Oligosaccharides Kit (Maltotriose, Dp3: R474140)</td>
			<td style="width:155px;">Supelco&#160;</td>
			<td>47265</td>
			<td style="width:303px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Oligosaccharides Kit (Maltotetraose, Dp4: R474135)</td>
			<td style="width:155px;">Supelco&#160;</td>
			<td>47265</td>
			<td style="width:303px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Disposable Pasteur Pipets, Glass, Short Tip</td>
			<td style="width:155px;">VWR</td>
			<td>14673-010</td>
			<td style="width:303px;">Wash before use</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:231px;">PYREX 13 x 100 mm Disposable Round Bottom Threaded Culture Tubes</td>
			<td style="width:155px;">Corning</td>
			<td>99447-13</td>
			<td style="width:303px;">Wash before use</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:231px;">PYREX 16 x 125 mm Disposable Round Bottom Threaded Culture Tubes</td>
			<td style="width:155px;">Corning</td>
			<td>99447-16</td>
			<td style="width:303px;">Wash before use</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Phenolic Caps/Closures with PTFE-Faced Rubber Liner</td>
			<td style="width:155px;">Kimble</td>
			<td>45066C-13</td>
			<td style="width:303px;">Wash before use</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Phenolic Caps/Closures with PTFE-Faced Rubber Liner</td>
			<td style="width:155px;">Kimble</td>
			<td>45066C-15</td>
			<td style="width:303px;">Wash before use</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Hamilton HPLC syringe</td>
			<td style="width:155px;">HAMILTON</td>
			<td>81265</td>
			<td style="width:303px;">volume 500&#160;&#956;L, needle size 22 ga&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Hamilton HPLC syringe</td>
			<td style="width:155px;">HAMILTON</td>
			<td>81165</td>
			<td style="width:303px;">volume 250&#160;&#956;L, needle size 22 ga</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Hamilton HPLC syringe</td>
			<td style="width:155px;">HAMILTON</td>
			<td>81065</td>
			<td style="width:303px;">volume 100&#160;&#956;L, needle size 22s ga&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Hamilton HPLC syringe</td>
			<td style="width:155px;">HAMILTON</td>
			<td>80965</td>
			<td style="width:303px;">volume 50&#160;&#956;L, needle size 22s ga</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Hamilton Calibrated Syringes</td>
			<td style="width:155px;">HAMILTON</td>
			<td>80300</td>
			<td style="width:303px;">volume 10&#160;&#956;L, needle size 26s ga&#160;</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:231px;">Petri Dish Glass 100mm x 15mm</td>
			<td style="width:155px;">GSC INTERNATIONAL INC</td>
			<td>1500-4</td>
			<td style="width:303px;">Wash before use, Step 1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Bard-Parker Surgical Blades</td>
			<td style="width:155px;">Fisher</td>
			<td>371310</td>
			<td style="width:303px;">Step 1</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Reacti-Therm Heating/Stirring Module</td>
			<td style="width:155px;">Pierce</td>
			<td>18870</td>
			<td style="width:303px;">Step 1, 4 and 7</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Heating Blocks</td>
			<td style="width:155px;">Fisher</td>
			<td>125D</td>
			<td style="width:303px;">Step 2</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">Pyrex fiber glass wool borosilicate pore size 8&#160;&#956;m</td>
			<td style="width:155px;">Aldrich</td>
			<td>CLS3950</td>
			<td style="width:303px;">Step 3</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Fused Silica CutterTubing cutter</td>
			<td style="width:155px;">alltech</td>
			<td>3194</td>
			<td style="width:303px;">Step 3</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Multi-tube vortexers&#160;</td>
			<td style="width:155px;">VWR</td>
			<td>444-7063</td>
			<td style="width:303px;">Step 6</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Lyophilizer 25EL Freezemobile</td>
			<td style="width:155px;">Virtis</td>
			<td>25EL</td>
			<td style="width:303px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;">Centrifuge</td>
			<td style="width:155px;">VWR</td>
			<td>Clinical 50</td>
			<td style="width:303px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:231px;"></td>
			<td style="width:155px;"></td>
			<td></td>
			<td style="width:303px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:231px;">LTQ Orbitrap Discovery</td>
			<td style="width:155px;">Thermo Fisher Scientific</td>
			<td></td>
			<td style="width:303px;">0</td>
		</tr>
	</tbody>
</table>

improved in-gel reductive &#946;-elimination for comprehensive o-linked and sulfo-glycomics by mass spectrometry

Separation of proteins by SDS-PAGE followed by in-gel proteolytic digestion of resolved protein bands has produced high-resolution proteomic analysis of biological samples. Similar approaches, that would allow in-depth analysis of the glycans carried by glycoproteins resolved by SDS-PAGE, require special considerations in order to maximize recovery and sensitivity when using mass spectrometry (MS) as the detection method. A major hurdle to be overcome in achieving high-quality data is the removal of gel-derived contaminants that interfere with MS analysis. The sample workflow presented here is robust, efficient, and eliminates the need for in-line HPLC clean-up prior to MS. Gel pieces containing target proteins are washed in acetonitrile, water, and ethyl acetate to remove contaminants, including polymeric acrylamide fragments. O-linked glycans are released from target proteins by in-gel reductive &#946;-elimination and recovered through robust, simple clean-up procedures. An advantage of this workflow is that it improves sensitivity for detecting and characterizing sulfated glycans. These procedures produce an efficient separation of sulfated permethylated glycans from non-sulfated (sialylated and neutral) permethylated glycans by a rapid phase-partition prior to MS analysis, and thereby enhance glycomic and sulfoglycomic analyses of glycoproteins resolved by SDS-PAGE.

Effect of Ethyl Acetate Treatment Prior to In-gel Reductive &#946;-Elimination
A representative mass spectrum of permethylated O-linked glycan samples released from bovine mucin using in-gel reductive &#946;-elimination is shown in Figure 3. The EtOAc wash of the gel pieces effectively removes SDS and polyacryl contaminants which interfere with subsequent MS analysis 27.
<img alt="Fig...

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Improved In-gel Reductive &amp;#946;-Elimination for Comprehensive O-linked and Sulfo-glycomics by Mass Spectrometry

In order to comprehensively explore the diversity of O-linked glycans, a new procedure for in-gel reductive &#946;-elimination, combined with permethylation and a rapid phase-partition method, is applied to the analysis of O-linked glycans directly released from glycoproteins resolved by SDS-PAGE and amenable to subsequent glycomic analysis by mass spectrometry.

Improved In-gel Reductive &#946;-Elimination for Comprehensive O-linked and Sulfo-glycomics by Mass Spectrometry

Separation of proteins by SDS-PAGE followed by in-gel proteolytic digestion of resolved protein bands has produced high-resolution proteomic analysis of ...

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Nucleophilic Substitution and Elimination Reactions of Alkyl Halides

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