PMID: PMC4261947-1-3

 

    Legend: Gene, Sites

Title : Comparisonof the Data with the 2012 ABRF Data and a Data Setfrom a Laboratory Participating in the 2012 ABRF Study

Abstract :

1. Asone of the 26 global laboratories that participated in the 2012 ABRFGlycoprotein Research Group (gPRG) study (the 2012 ABRF study), the qualitative and quantitative results werecompared to evaluate our glycoproteomic methods
2. The goal of the 2012ABRF study was to provide a global overview of glycoproteomics methodsusing a consensus among interlaboratory data
3. As a result, 57 N-glycanswere reported in total
4. Twenty six data sets collected from the participatinglaboratories were classified into four clusters from A to D basedon data similarity
5. The major cluster is C, where the data were summarizedfrom 21 laboratories, including our laboratory
6. According to abundances,N-glycans were grouped into three categories, including major, intermediate,and minor abundance structures
7. A separate result has been publishedby Behnken et al
8. They were also an ABRF-participatinglaboratory that identified 42 glycoforms of intact PSA /PSAH glycoproteinusing HR– ESI /TOF–MS. As shown in Supporting Information Figure 5A, the three studies reported85 total glycoforms associated with PSA and PSAH, with 29 common glycoforms
9. Seventeen additional glycoforms were commonly identified between the2012 ABRF study and this study
10. Forty six glycoforms were observedboth in the ABRF study and here
11. Eleven glycoforms were detected onlyin the ABRF study
12. Twenty two structures were unique to this study
13. Three glycoforms were reported by Behnken et al. and were observed in our study but were not described inthe ABRF study
14. Our study and that by Behnken et al. study had 32 common glycoforms
15. Ten glycoforms were describedin Behnken et al.’s study but were not observed in our study,of which four were described in the ABRF study
16. This discrepancy maybe due to the use of different methods: bottom-up gycoproteomics inthis study and top-down glycoproteomics in the Behnken et al. study
17. As shown in SupportingInformation Figure 5B, the relative abundances of 18 major/intermediateN-glycans appeared to be comparable with that in the 2012 ABRF study
18. In particular, the N-glycans HexNAc3Hex4dHex1NeuAc1, HexNAc4Hex5dHex1NeuAc2,HexNAc5Hex3dHex1NeuAc1, and HexNAc5Hex4dHex1NeuAc1 wereobserved with a very high overlap in intensities
19. From minor N-glycans,we noticed that 6 of the 13 missing structures were sulfated/phosphorylatedN-glycans with very low intensities
20. One sulfated/phosphorylated glycoform,HexNAc5Hex4dHex1s/p , was reported in the 2012 ABRF study as beingless than 1%, but it is present in PSA at approximately twice theamount as that in PSAH
21. This particular glycoform was observed inour analysis and with a similar intensity profile variation
22. Behnken et al. reported a single analysisof quantitation; thus, no variation was inserted (Supporting Information Figure 5C)
23. Among the 32 common glycoformsthat were observed in our study, most of them showed a comparabletrend of intensities between PSA and PSAH
24. With regard to the 18 major/intermediateglycoforms defined by the 2012 ABRF study, 16 glycoforms were observedby Behnken et al., whereas 2 major/intermediateglycoforms were not reported, including HexNAc2Hex5 and HexNAc4Hex4dHex1.
25. Most of the major/intermediate glycoforms show comparable abundanceprofiles except for HexNAc4Hex5dHex1NeuAc2 , in which its abundancein PSA appeared to be 4.60-fold lower when comparing this study andthe 2012 ABRF study

Output (sent_index, trigger, protein, sugar, site):

• 8. glycoforms, , ESI, -, -

Output(Part-Of) (sent_index, protein, site):

*Output_Site_Fusion* (sent_index, protein, sugar, site):

 

Protein	NCBI ID	SENTENCE INDEX