The sampling size for this study was 10 women. Do you think that this sample size is large enough to draw definitive conclusions?
What is the significance of the serine residue phosphorylation site? I thought it was interesting that so many of the proteins discovered were phosphorylated at this site.
The aim of this study was to investigate the total protein expression patterns and phosphoprotein expression changes just before and after vaginal delivery and to identify the proteins that are important for maintaining pregnancy. I was curious as to why they chose those particular points during pregnancy if they were looking to identify pregnancy maintenance. Especially considering that one day before the baby is delivered, the body is preparing to not be pregnant any longer.
Additionally, I wondered whether they took into consideration different kind of diets and hydration levels in accordance to urine protein concentration, as this seems to me like it could have an influence.
In some women it can be difficult to predict exactly what day they will go into labor, which would have made taking a urine sample one day before delivery difficult. If these women were undergoing induced labor, would that have changed the phosphoprotein composition of their urine?
Also, do you think there were enough considerations (previous pregnancies, diet, stress levels, etc) in place to make these differential protein expression levels in ten women valid?
I thought the paper by Zheng et al. was interesting as it allowed comparison between the urine proteome and phosphoproteome before and after vaginal delivery. If the goal of this study is to identify proteins uniquely involved in pregnancy I wonder whether their "after" endpoint of one month following delivery is long enough. If a woman is still breastfeeding she will still be producing proteins associated with pregnancy, and therefore, these may be overlooked by their analysis.
I also was a little skeptical of their comparison between their results and previous urine proteome studies. As they note they were able to identify many more proteins due to their new methods. Therefore, how are they able to tell which proteins are new because they are associated with pregnancy and which are new due to the improved methodology?
Why, in the Zheng study, is it advantageous to study the phosphoproteome in particular? What does this study gain from looking at the phosphorylation of proteins over, for example, glycosylation as a post translational modification?
Do you think that there is any risk for inaccuracies in the data as a result of pooling the samples? Would there be any advantages to testing women individually? If so, could this lead to medical advancements in regards to abnormalities in a pregnancy?
The review paper stated that recent model organism mass spectrometry-based protein identification experiments ranged from 50-80% coverage of the proteins encoded by the genome. While a promising start, do you think yields of 50% coverage mean this field is too underdeveloped to be utilized in scientific research at this time? What problems are causing this low coverage by MS methods?
Pregnancy is a fascinating thing to study especially at the macromolecule level. Because they tested gross protein levels based on novel findings and pre- post-pregnancy states, this paper is not specific to variables associated with their samples. I think this experiment could be expanded on, especially taking into the account the amount/types of prenatal vitamins, diet and environmental factors.
The experiments discussed in the article by Zheng, et al., filtered out low molecular weight peptides. They described this as being important, but why?
Also, do you think they'll proceed by using these same protocols at different stages during pregnancy? If so, how would this phosphoproteome be useful?
I am intrigued by the Zheng, et al. findings. It seems like impact and methodological soundness is limited by the fact that they are examining a transient physiological state, however. I'm wondering how proteomic analysis might be useful in other applications -- how, for instance, it is powerful in a way that SNP analysis or molecular genetics experiments are not.
In the paper, it stated that intermediate cells have a low efficiency for reprograming. Do you know why this is? Does this fact hinder, other research related to pluripotency and intermediate cells?
The authors argued that the information gleaned from pregnant women's urine proteome and phosphoproteome could be used, basically, as a reference point to diagnose pregnancy related issues. However, they also cited individual variation. That along with a very small sample size would make it hard to come to any definitive conclusions about 'normal' levels. Thus, how could this information actually be used on a large scale? Would each woman have to give a urine sample, or multiple samples, before/during her pregnancy? And how feasible, cost and time wise, would it be to constantly be analyzing her urine?
In the paper, the authors say “different proteins observed in urine samples are likely due to differences physiologies state of pregnancy and non-pregnancy”. I wonder whether this statement considers different nutritional conditions in pregnant patients groups or in non-pregnant patient groups.
This study discussed the differences in urinary proteins between healthy pregnant and non-pregnant women but it did not talk about whether there were individual differences between the women. Do most healthy individuals have similar amounts of the different urinary proteins? Or is there a lot of variation between individuals?
The authors mention that this study identified the largest catalog of proteins from the urinary proteome, and that employing multiple gel pre-fractionations reduced the complexity of the sample. Why wouldn't using many strips per lane make it more complex?
Also, just out of curiosity, are the pregnancy-specific proteins (placental, etc.) that are found in women what are screened for in home-pregnancy tests?
Grossest phrase in a paper to date: "pooled urine samples"
The authors seem interested in creating a "profile" for phosphopeptides in the urine of pregnant and non-pregnant patients. But they only sampled urine immediately before and after giving birth. Doesn't this miss the possibility of expression of certain proteins increasing and decreasing over the first two trimesters? It seems to me that healthy pregnancy is about more than just the last couple of days; it would be useful to understand the expression levels across the whole pregnancy.
So the aim of this study was to investigate the total protein expression patterns and phosphoprotein expression changes just before and after vaginal delivery, but how can they know how crucial each change is for maintaining "healthy" pregnancy since they do not sample women with "unhealthy" pregnancy? What can they achieve with this knowledge? Are they ways they can induce such changes for clinical purposes?