GlycoPOD
Abstract
Recently, carbohydrate chains occupy truly significant positions in various
fields of life sciences and biotechnology. Accordingly, an increasing number ofstudents and researchers are conducting experiments on carbohydrate chains.
However, we sometimes encounter a common beginner’s feeling that experiments
in glycoscience are not so easy to perform satisfactorily. In molecular biology, mostof the reagents are commercially available as a series of kit and all you need is tofollow the operating manual provided with the distributors of the reagents. In
glycoscience, in contrast, Materials and Methods in a professional journal may not
be enough to provide beginners with sufficient information about theexperimental procedures of their interest.
GlycoPOD (GlycoScience Protocol Online Database) project started in May 2009as a part of the program of the Japan Consortium for Glycobiology and
Glycotechnology Data Base (JCGGDB), aiming to fill the gaps between thebeginners and experts by delivering the accumulated knowledge and skills of theexperts to the beginners through internet communication under the catch-phraseof “Follow the flow chart and you will get the goal directly”. Now, more than 150
experts (JCGG members) have been involved in the GlycoPOD activity so far.

Features of GlycoPOD
As of March 1, 2017, GlycoPOD (see Figure 1) provides 262 protocols.
As an on-line protocol, GlycoPOD has a unique architecture. It consists of threemain parts, “Introduction“, “Protocol” and “References” (see Figure 4 & 10). In“protocol”, all the experimental procedures are documented in flow charts withcomments, which contain precious tips for success.
If you choose “Authors” at the top page, you will see the name of all authors listed
in alphabetical order (see Figure 2).
If you click “`KeyWords” button, all the experimental procedures listed in“protocol” are broken down into individual experimental elements (parts) and1

they are reorganized in alphabetical order (see Figure 3). “KeyWords will be
useful in case you cannot find the exact protocol you need in “Protocols (maintext)”, or you want to modify the experimental conditions of the original protocol
and others.
Here, we would like to introduce a general outline of GlycoPOD.
1. Introduction (see Figure 5 & 11)
This section contains a summary of the method or outline of the major procedures
involved in the protocol.
2. Protocol (see Figure 4 & 10)“Protocols” has 11 sections, Category, Protocol Name, Authors, Keyword, Reagents& Instruments, Methods (Comments), Note, Initial Amounts, Discussion, andFigure & Legend.
2-1. Category (17 categories)
All the protocols (216 as of March 1, 2017) are organized into 17 categories of thefollowing:
Isolation & structural analysis of glycans

N-Glycans
O-Glycans
Glycolipids and related compoundsGlycosaminoglycans
Glycosyltransferases & related proteins
Nucleotide sugar transporters
Sugar binding proteins
Matrices & cellular trafficking
Biosynthesis & Metabolism
Glycogene transgenic animals
Glycosidases & related proteins
GPI anchored proteins
Large scale preparation of glycans, glycoproteins & glycolipids
Roles of glycans during microbial infection
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Plant cell Wall analysis
Glyco-proteomic mass spectrometry protocols
2-2. Key Words
A few important key words in protocols are listed in this section.
2-3. Reagents & Instruments
Recommendable reagents or instruments for the experiment are itemized with
supplier/manufacturer names.
2-4. Methods (Procedures)This is the main section of the protocol and explains in detail the individual steps
necessary to carry out the experiment.
2-5. Comments (for each procedure) (see Figure 7 & 13)
Any hints and tips that help improve your method are described.
2-6. Notes (see Figure 14)
Overall comments or any other special instructions for the method are describedin this section.
2-7. Initial AmountThe amount of samples required for analysis is described here.
2-8. Discussion
The interpretation of the results are explained in this section.
2-9. Figure & Legend
3. Reference
All references of figures, tables, or text passages cited in protocols are listed inthis section. PubMedIDs are indicated at the end of each reference, and clicking
the ID links the Pubmed pages (see Figure 8 & 15).

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By clicking “KeyWords”, you can see individual experimentalelements (parts) in protocols.

In “Protocols”, all theprotocols are listed in
categories as below.

In “Authors”, you will see the name of
all authors listed in alphabetical order.

Figure 1Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Clicking the Comment,
you can see notices
for each step.

Figure 7

Clicking the PMID links to show
the PubMed page.

Figure 8

Click this icon to access the protocol.

Figure 9

Figure 10

Figure 11

Figure 12

Clicking the Comment,
you can see notices
for each step.

Figure 13

Figure 14

Clicking the PMID links to show
the PubMed page.

Figure 15