Limits...
Can museum egg specimens be used for proteomic analyses?

Portugal SJ, Cooper HJ, Zampronio CG, Wallace LL, Cassey P - Proteome Sci (2010)

Bottom Line: We found that some of the expected key eggshell proteins (3 out of 11) were not present in the samples of museum quail egg.There was no pattern in the absent proteins in the sense of protein function or where they are located within the eggshell.We conclude it is likely that such studies on museum specimens using a proteomic approach will be limited in coverage of proteins and may, therefore, be misleading.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Centre for Ornithology, School of Biosciences, College of Life and Environmental Sciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. S.Portugal.1@bham.ac.uk.

ABSTRACT

Background: Mass spectrometry and proteomic analyses have become powerful tools for the analysis of proteins and peptides. Investigation of proteins contained in the various layers of the avian eggshell has focused entirely on domesticated species. It has been widely assumed that this existing research can inform the study of wild bird species despite the fact that the vast majority of the diversity in avian species (~95%) exists outside the Orders to which domestic and poultry species belong. Museum collections offer a potentially valuable source of material for studying composition of wild avian eggshell matrix proteins. We used museum and fresh eggshells of common quails Coturnix coturnix to compare the protein composition of their organic matrices. Four eggs of domestic chickens were analysed simultaneously as a control for comparison to the fresh and museum quail eggs. The determination of the proteins was carried out using enzymatic cleavage followed by high-performance mass spectrometry.

Results: We found that some of the expected key eggshell proteins (3 out of 11) were not present in the samples of museum quail egg. These proteins were either entirely absent from the museum eggs or the technique was unable to detect them. There was no pattern in the absent proteins in the sense of protein function or where they are located within the eggshell.

Conclusion: We conclude it is likely that such studies on museum specimens using a proteomic approach will be limited in coverage of proteins and may, therefore, be misleading.

No MeSH data available.


Distribution of protein types in the avian eggshell. Differential localised pattern for eggshell matrix proteins within the avian eggshell. Data from different studies (see Hincke et al [3]) are summarised to demonstrate the localisation of the eggshell proteins through the 3 main layers; PL (pallisade layer), ML (mamillary layer) and SM (shell membrane), plus the C (cuticle). The scanning electron microscope image is taken from Hincke et al [3].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2927511&req=5

Figure 1: Distribution of protein types in the avian eggshell. Differential localised pattern for eggshell matrix proteins within the avian eggshell. Data from different studies (see Hincke et al [3]) are summarised to demonstrate the localisation of the eggshell proteins through the 3 main layers; PL (pallisade layer), ML (mamillary layer) and SM (shell membrane), plus the C (cuticle). The scanning electron microscope image is taken from Hincke et al [3].

Mentions: Based on Mann et al. [2,16], 11 key eggshell proteins were selected to test for their presence in both fresh and museum quail egg specimens (Fig. 1, Additional File 1). Database searches (Swissprot and NCBInr) were conducted using the MASCOT (Matrix Science, London, UK). Variable modifications were N-acetyl and oxidation (M). The peptide tolerance was 5 ppm and the MS/MS tolerance was 0.5Da. One missed cleavage was allowed. BLAST analysis of identified proteins was performed with the programme provided by the NBCI against the non-redundant database for all organisms. Protein identifications provided by MASCOT software were accepted if the data set contained at least two peptides with a MASCOT score > 25 at P > 0.01. Subsequent reverse searches of all data showed the number of false positives to be less than 1%.


Can museum egg specimens be used for proteomic analyses?

Portugal SJ, Cooper HJ, Zampronio CG, Wallace LL, Cassey P - Proteome Sci (2010)

Distribution of protein types in the avian eggshell. Differential localised pattern for eggshell matrix proteins within the avian eggshell. Data from different studies (see Hincke et al [3]) are summarised to demonstrate the localisation of the eggshell proteins through the 3 main layers; PL (pallisade layer), ML (mamillary layer) and SM (shell membrane), plus the C (cuticle). The scanning electron microscope image is taken from Hincke et al [3].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2927511&req=5

Figure 1: Distribution of protein types in the avian eggshell. Differential localised pattern for eggshell matrix proteins within the avian eggshell. Data from different studies (see Hincke et al [3]) are summarised to demonstrate the localisation of the eggshell proteins through the 3 main layers; PL (pallisade layer), ML (mamillary layer) and SM (shell membrane), plus the C (cuticle). The scanning electron microscope image is taken from Hincke et al [3].
Mentions: Based on Mann et al. [2,16], 11 key eggshell proteins were selected to test for their presence in both fresh and museum quail egg specimens (Fig. 1, Additional File 1). Database searches (Swissprot and NCBInr) were conducted using the MASCOT (Matrix Science, London, UK). Variable modifications were N-acetyl and oxidation (M). The peptide tolerance was 5 ppm and the MS/MS tolerance was 0.5Da. One missed cleavage was allowed. BLAST analysis of identified proteins was performed with the programme provided by the NBCI against the non-redundant database for all organisms. Protein identifications provided by MASCOT software were accepted if the data set contained at least two peptides with a MASCOT score > 25 at P > 0.01. Subsequent reverse searches of all data showed the number of false positives to be less than 1%.

Bottom Line: We found that some of the expected key eggshell proteins (3 out of 11) were not present in the samples of museum quail egg.There was no pattern in the absent proteins in the sense of protein function or where they are located within the eggshell.We conclude it is likely that such studies on museum specimens using a proteomic approach will be limited in coverage of proteins and may, therefore, be misleading.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Centre for Ornithology, School of Biosciences, College of Life and Environmental Sciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. S.Portugal.1@bham.ac.uk.

ABSTRACT

Background: Mass spectrometry and proteomic analyses have become powerful tools for the analysis of proteins and peptides. Investigation of proteins contained in the various layers of the avian eggshell has focused entirely on domesticated species. It has been widely assumed that this existing research can inform the study of wild bird species despite the fact that the vast majority of the diversity in avian species (~95%) exists outside the Orders to which domestic and poultry species belong. Museum collections offer a potentially valuable source of material for studying composition of wild avian eggshell matrix proteins. We used museum and fresh eggshells of common quails Coturnix coturnix to compare the protein composition of their organic matrices. Four eggs of domestic chickens were analysed simultaneously as a control for comparison to the fresh and museum quail eggs. The determination of the proteins was carried out using enzymatic cleavage followed by high-performance mass spectrometry.

Results: We found that some of the expected key eggshell proteins (3 out of 11) were not present in the samples of museum quail egg. These proteins were either entirely absent from the museum eggs or the technique was unable to detect them. There was no pattern in the absent proteins in the sense of protein function or where they are located within the eggshell.

Conclusion: We conclude it is likely that such studies on museum specimens using a proteomic approach will be limited in coverage of proteins and may, therefore, be misleading.

No MeSH data available.