MIAPE satisfaction survey
       
In November 2008, before the presentation of the results of the ProteoRed Multicenter Experiment 2008 (PME'08), we elaborated this survey in order to evaluate two aspects:
       
    - the MIAPE generator tool  
       
    - the MIAPE guidelines  
       
The survey was completed by 31 proteomic experts from 17 Proteomics facilities:
    Bilbao: CIC BioGune, UPV  
    Pamplona: CIMA  
    Valencia: CIPF, UV  
    Madrid: CNB, CBM, PCMUCM  
    Barcelona: HUVH, CSICUAB, PCB, UPF, IBBUAB, UB  
    Alicante: UA  
    La Coruña: INIBIC  
    Geneva: SIB  
       
Here you can see the results:
  We apologize for possible incorrect usages, as we didn´t have the time for a throughout revision of the texts sent  
       
MIAPE reports in your laboratory
 
You think that the generation of MIAPE compliant reports is useful...
  ...as a results report for my customers 22 55%
  ...for my own purposes in my lab 14 35%
  ...for other purposes (specify them)... 2 5%
  ...not. It is not useful because... 2 5%
Explanations
 
They can think that MIAPE is a quality label of our lab, although they don't understand MIPAE
A MIAPE report is rigth now, by itselt the best quality label possible.
because, are not very clear even the answers for the questions
the quality of the results is not enhanced by providing a completed technical information
Most customers do not know what is a MIAPE report so for them it is just more paper until they need to publish some data 
As for today, none of our customers had the need for MIAPE documentation.
Sometimes, it was not very clear for me to compile the MIAPE document and as I compile two document (MS and informatic)some informations were asked twice.
They will obtain the information needed in a readeable format
They feel more confident at the time to publish the results. Many magazines ask for some of those data.
I believe it can be a good think for customer as they may know ny single details about how the sample has been processed.
 
In your opinion, is the generation of MIAPE compliant reports a quality label for your customers?
  Yes, sure 9 30%
  Yes, I think 12 40%
  No 5 17%
  Not yet 4 13%
Explanations
 
They can think that MIAPE is a quality label of our lab, although they don't understand MIPAE
A MIAPE report is rigth now, by itselt the best quality label possible.
because, are not very clear even the answers for the questions
the quality of the results is not enhanced by providing a completed technical information
Most customers do not know what is a MIAPE report so for them it is just more paper until they need to publish some data 
As for today, none of our customers had the need for MIAPE documentation.
Sometimes, it was not very clear for me to compile the MIAPE document and as I compile two document (MS and informatic)some informations were asked twice.
They will obtain the information needed in a readeable format
They feel more confident at the time to publish the results. Many magazines ask for some of those data.
I believe it can be a good think for customer as they may know ny single details about how the sample has been processed.
 
If you are not currently generating MIAPE compliant reports, when do you think you will be able to do it?
  Never 0 0%
  on a short term 14 56%
  on a medium term 7 28%
  on a long term 4 16%
Explanations
 
I am not using them now because a lack of time to fill them.
we are currently generating MIAPE
if is necesary for publications
We are currently generating MIAPEs
we hope!
When we have more manpower to do it regularly
It depends on how generalist journals in a future expand the requests for information about the experiments, because our customers are more focused on this broad range papers, that commonly doesn´t request too much information about each experiment involved.
We are thinking about what kind of report we had to furnich to our customer.
Our currently system will be used until the en of 2008
depends on the customers
SHORT-MEDIUM term. 
Our users customers do not in general ask for it. Anyhow, I think it can be send together with the final report. another posibility is to send a MIAPE to a customer, and do not send it any longer as far as there is no change in the way of processing sample, and only when a change is done, send last version. I am thinking about neighbours that send samples in regular bases and I don´t think is useful to send the same MIAPE each time they send us samples.
It is time consume and We will do just in the case that they ask for it
In our lab we are generating Miape
In our lab we are currently generating MIAPE compliant reports
I usually generate miape compilant reports
 
Use of the MIAPE generator tool
 
Are you using the MIAPE generator tool in your lab?
 

Yes

 12 55%
  No 10 45%
Explanations
 
Yes, but sometimes
Only for Proteored assays
We have some MIAPE docs created, but without use.
Not yet. Possibly in a future
Our currently system will be used until the en of 2008
very seldom yet
at this moment, we don´t use the Miape generator tool for MS report result
 
How many times have you used the MIAPE generator tool?
  Never 0 0%
  1 1 4%
  2 2 7%
  3 2 7%
  4 0 0%
  5 1 4%
  More than 5 5 18%
  Only for the ProteoRed multicentric Experiments 13 46%
  I usually generate MIAPEs with the tool 4 14%
Explanations
  Mainly for ProteoRed multicentric experiment, and very seldom for others.
 
If you are NOT using the MIAPE generator tool frecuently, specify why
  It's time consuming 13 37%
  It's not necessary 1 3%
  It's not a quality label for us 3 9%
  We will do it, but now... 5 14%
  It's necessary to improve the tool 2 6%
  Our customers don't want all information required in the MIAPE guidelines 11 31%
Explanations
 
Some users only realize on the importance of the information provided when the prepare manuscripts.
No time and we have had other priorities but we are planing to start using them
I am using it
We had other tools for the same purpose, but Miape generator is much better than our tool.
Until now, we don't need to use it but we are evaluating what kind of report we have to furnich to our customer
Our currently system will be used until the en of 2008
and our customers not always need all the data. They prefer the identification of proteins as soon as possible.
At firs it´s necessary to create different templates for the different aplications
As explained before, it may be inplemented in next generation reports to be in practize hopefully soon.
I generate Miape
We are using the MIAPE generator tool
I usually generate MIAPEs with the tool. I think it is time consuming but finally the information is well arranged.
 
Please, specify the weak spots of the MIAPE generator tool
 
It is not very friendly
I haven't used the MIAPE enough to answer this question
none
.
it´s time consuming. 
our customers don´t want all information requiered.
Maybe a little too difficult for non-experienced customers
Time consuming, some times questions are repeated in a different part of the MIAPE and sometimes it is not very clear what do I have to fill in each form
I don't know. I've used infrequently.
clearity of the questions
One cannot see the extent of all the different tabs to be filled out. The navigation tree has definetely improved that but it is still not very user friendly
It should be automatic (imported from MS data). The required information is very redundant, the filling is not intuitive and you lose in the window when you back to the menu
None
time consuming and it don't our complete report, only a part of it.
We do not use it yet
It could be interesting to save reports in PDF format. 
Also, only filled fields (specific of a given methodology) must be shown
Time consuming
As I don not have much experince using it.I would not know 
Much data needed and sometimes I don't know where find it.
In some points there is redundant information
I am not a direct user.
We have to type all information by hand. There is no controlled vocabulary (the person filling the form can express things that are not understandable and thus are not comparable). Ideally I would like to read one MIAPE document and easily compare with another one. If 2 people fill the same form, may not be necessarily comparable.
Not always you know what information is asked in some fields. 
when we are generated Miapes if we don´t create in the moment the session ends
When we are generate MIAPEs with the generator tool if we don´t create in the moment the tool failed.
-Sometimes depend on the technique, I don`t Know what is the minimal information I have to put. 
have unsuful information 
Time consuming 
The attach files (format, http, etc)
Time consuming 
Sometimes it is not very clear what to fill
 
Please, specify the strong points of the MIAPE generator tool
 
Provide all analytical parameters required to define the experiments
I haven't used the MIAPE enough to answer this question
none
.
it´s a good report (but sometimes too long)
Is aquality label
All data integrated in a link, easy to check and useful to see
I don't know. I've used infrequently.
I don´t konow...
It is good to have a consensus tool that is the same format for all labs. Being able to store and use again info from previous MIAPEs.
All MS and technical information is contained in the report
None
useful reprot for our cutomers
We do not use it yet
It´s a fast method to generate reports.
Once compile, all the informations are collected
Good structure
it's easy to use
The trazability of the analyses and the generated data
Although I did not use it by myself, I believe once the template is done, is rather easy to change and create a new one.
Nice interface.
If you have one previously done, is easier to fill the next one
All results are grouped
With the MIAPE report we have all the results compiled.
The information is wellarranged. 
The customers have the protocol of the technique and the results enclosed in a project. 
You can save a MIAPE template. 
In the Miape, you can storage a most of the information from a proteomic experiments and let recovery this information
Helps to organize the information
 
Once you have created your own MIAPE templates according to your different techniques in your lab, in your opinion, how long does it cost to generate a new MIAPE compliant report?
  Less than 5 min 4 17%
  5 min - 10 min 3 13%
  10 min - 20 min 6 26%
  20 min - 30 min 2 9%
  30 min - 45 min 6 26%
  more than 45 min 2 9%
Explanations
 
But additional information must be provided to users, sometimes additional reports are requiered in is particular experiments.
don't know
We do not use it yet
I have no idea because it was the first time that I use it
I am not a direct user.
Depends if I can do a copy-paste of a old document or not.
Depend on the samples you have and the different techniques, but probably more than 45 min.
 
And if you don't add the results in the MIAPE report, that is, only information about the protocol or techniques followed to reach these results, how long dos it cost?
  Less than 5 min 3 12%
  5 min - 10 min 8 33%
  10 min - 20 min 4 17%
  20 min - 30 min 4 17%
  30 min - 45 min 2 8%
  more than 45 min 3 13%
Explanations
 
it´s depends. may be 10 min or 2 hours...
We do not use it yet
I have no idea because it was the first time that I use it
I am not a direct user.
The same time of doing the MIAPE report (since I will have to write one of the 2).
But is easier to the customer to follow all the experiment
If only you add the protocol or techniques you can load a previous miape and you can only change the differences.
 
Details of the MIAPE generator tool
 
Maybe sometimes it is not very clear what do I have to fill in each form. Evaluate the level of clarity (from 1 to 10)
 
  1 2 3 4 5 6 7 8 9 10 N/A Mean
Clarity 0% (0) 3,7% (1) 3,7% (1) 14,81% (4) 18,52% (5) 37,04% (10) 14,81% (4) 3,7% (1) 0% (0) 0% (0) 3,7% (1) 5,46
 
Is it useful the capability of load previously created information in order to create new MIAPE reports?
 
Yes, it is necessary since the protocols are normalized in the lab and most parameters are common to conventional analyses
Very useful
Yes
.
YES
Yes
Yes
Yes, it is very useful in that regard
yes
Yes
yes
Yes it is very useful.
yes, of course
Yes
Yes, for sligly modified protocols or techniques
Yes, it is very useful
I think is usefull but I had not the occasion to try.
yes
I am not a direct user. But have been told it is.
Yes, I think it´s helpful
yes!
Yes
Is more useful
Is more useful
Yes, because you spend less time in create the miape report
Is very usuful.
Yes, sure
 
Evaluate the following aspects about the MIAPE generator tool (1:bad- 10:good)
 
1 2 3 4 5 6 7 8 9 10 N/A Mean
useful 0% (0) 3,7% (1) 0% (0) 0% (0) 11,11% (3) 18,52% (5) 22,22% (6) 14,81% (4) 18,52% (5) 3,7% (1) 7,41% (2) 7,04
user friendly 0% (0) 0% (0) 7,41% (2) 11,11% (3) 29,63% (8) 22,22% (6) 11,11% (3) 7,41% (2) 7,41% (2) 0% (0) 3,7% (1) 5,73
boring (1 very boring - 10 not boring) 11,11% (3) 3,7% (1) 14,81% (4) 14,81% (4) 18,52% (5) 11,11% (3) 11,11% (3) 0% (0) 3,7% (1) 0% (0) 11,11% (3) 4,42
indispensable 3,7% (1) 3,7% (1) 0% (0) 14,81% (4) 40,74% (11) 3,7% (1) 14,81% (4) 7,41% (2) 0% (0) 0% (0) 11,11% (3) 5,17
support in case of problems 0% (0) 0% (0) 0% (0) 3,7% (1) 11,11% (3) 11,11% (3) 14,81% (4) 18,52% (5) 11,11% (3) 18,52% (5) 11,11% (3) 7,58
time consuming 3,7% (1) 3,7% (1) 3,7% (1) 0% (0) 11,11% (3) 33,33% (9) 18,52% (5) 14,81% (4) 7,41% (2) 0% (0) 3,7% (1) 6,15
confusing 0% (0) 3,7% (1) 3,7% (1) 11,11% (3) 29,63% (8) 37,04% (10) 0% (0) 3,7% (1) 3,7% (1) 0% (0) 7,41% (2) 5,36
 
Some comments about MIAPE Gel Electrophoresis (MIAPE GE) forms...
 
No comments additional to the already answered questions.
We don't have gel service
none
.
very complete but time consuming... 
Not used
We are testing the tool
N/A
very laboriously, innecesary the customers dont understand the MIAPes
No
none
I did not use them
image loading is most time consuming stage
Nothing
too much steps involved. Somehow cryptic navigation across the different steps (going back or forward...)
None so far
never used it
Easy and quick to make it
I am not a direct user.
I haven´t used it
I didn't fill this one.
Ok
In my opinion this is the more complete MIAPE.
In my opinion it is the most complete
I think Miape Gel Electrophoresis is very clear and if your experiments are very similar you can load previously created information in order to spend less time.
Montse´s coments
Very long, takes a lot of time if you don´t have a template
 
Some comments about MIAPE Gel Informatics (MIAPE GI) forms...
 
No comments additional to the already answered questions.
We don't have gel service
none
.
Some information is repeated in MIAPE GE
Not used
We are testing the tool
N/A
very laboriously, innecesary the customers dont understand the MIAPes
Nothing
none
I did not use them
OK
Nothing
same as above
None so far
never used it
Easy and quick to make it
I am not a direct user.
I haven´t used it
I didn't fill this one.
Confuse about the information that you should provide of the spots
In our lab don´t use this MIAPE
In our lab don´t use this Miape
It is not very clear what do I have to fill in MIAPE Gel Informatics in Data reporting card. I don`t know exactly how I have to add the results.
Montse´s coments
No problems
 
Some comments about MIAPE Gel Informatics (MIAPE MS) forms...
 
No comments additional to the already answered questions.
Some times it is not clear what to put in each question but I haven't use it a lot
none
.
some items are not clear and depends on each MS´s parameters
Very useful.
We are testing the tool
N/A
nothing
Nothing
none
There are too many options available once you have selected a mass spectrometer that would correspond to other types of spectrometer
OK
Nothing
same as above
None so far
Once one page was compile you have to save and go back to continue, is not very logic for me. each time you have to enter a name, is not always very clear the name of what.
I don't know if some of the data relating to the Peak list generation section are always necessary for the user.
I am not a direct user.
As there are different analyzers and ways of sample introduction (LC coupled on-line/off-line to the MS), it´s not clear where the important parameters should be included
There were some redundant information with the MIAPE MSI (or at least it was not clear for us).
I don´t use it
In this MIAPE the information for the customer could be better and could be reflect for example the gradient of the HPLC, the time, etc........
In my opinion missing information for the user and plenty of others who do not need
I think MIAPE Mass Spectrometry was more clear if the different techniques will be separated.
Some parameters aren´t important. 
Perhaps the scheme could be more clear, and some step could be removed 
The vendors should provide all the MIAPE information regarding equipment and software.
 
Some comments about MIAPE Gel Informatics (MIAPE MSI) forms...
 
No comments additional to the already answered questions.
Some times it is not clear what to put in each question but I haven't use it a lot
none
.
Some information is repeated in MIAPE MS
Very useful
We are testing the tool
N/A
nothing
Nothing
none
No comments
OK
Nothing
same as above
None so far
Some parts to compile were a repetition of the MIAPE mass spectrometry forms
In this MIAPE document, the section: 
#The output from the procedure# 
It?s boring, complicated and time consuming if the experiment has many proteins to analysis and if it?s needed for every protein. Probably it?s very important but in practice, I don?t use it. 
And, I ask for apologies but, I don?t know where to find some of the requested data. 
I am not a direct user.
Including the results it´s time consuming
There were some redundant information with the MIAPE MS.
I don´t use it
This MIAPE is correct.
This Miape is correct
I don`t know exactly which is the minimal information I have to put for protein and peptide results
Is better than Miape MS. It include all interesting information about bioinformatic tools and results
Some things are redundant with MS section?
 
Next developments of the MIAPE generator tool
 
Evaluate the usefulness of the following improvements
 
1 2 3 4 5 6 7 8 9 10 N/A mean
MIAPE comparator tool (already implemented) 0% (0) 0% (0) 0% (0) 3,7% (1) 3,7% (1) 3,7% (1) 29,63% (8) 11,11% (3) 7,41% (2) 11,11% (3) 29,63% (8) 7,53
To import automatically identification results to the MIAPE MSI 0% (0) 0% (0) 0% (0) 0% (0) 0% (0) 7,41% (2) 11,11% (3) 33,33% (9) 7,41% (2) 14,81% (4) 25,93% (7) 8,15
To generate a Materials and Methods paragraph in natural language from MIAPE information 3,85% (1) 3,85% (1) 0% (0) 3,85% (1) 3,85% (1) 7,69% (2) 7,69% (2) 19,23% (5) 15,38% (4) 23,08% (6) 11,54% (3) 7,57
To export MIAPE information in a data standard schema such as GelML or PRIDE 0% (0) 0% (0) 0% (0) 0% (0) 12% (3) 4% (1) 20% (5) 20% (5) 8% (2) 8% (2) 28% (7) 7,44
To import MIAPE information from a data standard schema such as GelML or PRIDE 0% (0) 0% (0) 0% (0) 0% (0) 20% (5) 8% (2) 12% (3) 16% (4) 4% (1) 4% (1) 36% (9) 6,81
To import MIAPE information from a predefined excel spreadsheet template 3,85% (1) 0% (0) 0% (0) 3,85% (1) 15,38% (4) 11,54% (3) 11,54% (3) 11,54% (3) 15,38% (4) 11,54% (3) 15,38% (4) 7
 
Additional comments
 
Comments, criticisms, advices...
 
Thanks for your effort, you made a great job. It will be proved that MIAPE application will help a lot to all of us.
I think you are doing a good job and at least in my case I have to use it more before I can criticize MIAPE generator
.
useful but time-consuming. Maybe one could unify GE and MS to avoid repeating information in GEI and MSI
I think that is an useful tool, but is also time consuming and especially the MS blocks should be eventually integrated in the vendor´s software.
We are testing the tool
We use the MIAPE only for the ProteoRed multicentric Experiments and until today there has been no customer who has requested it. 
Then we do not believe that it is necessary for our customers yet.
is time consuming for the technical and not ussefull for customers.
Nothing
I had never done a miape and at first I thought it complicated.
Most important for us is the time consuming, because it isn't the only report for our customers and for this the generation of MIAPE documents is often show like a double time consuming
We do not use that much at the moment
We have not as much "contact" as we wish with MIAPE reports because our customer do not need them.
Conclusions from our la¨b: grat potential, good tool, needs maturing process
Well done!. In my view at the start what it might seem a time consuming task , in the end it is very helpful.
I tried to compile the questionnaire but to be onest it was the first time that I use MIAPE document, so I think a have not enough experience to answer to some questions.
All the new tools that automatically import data, make MIAPE reports easier and more convenient to use in a routine basis
I think proteomics is still a not fully standarized technology. It may due to the intrisic complexity of the proteome itself, so a miriad of protocols, methods etc. have to be used in orther to get a proper approach to analyze different type sample. These differences may be well reflected on the MIAPE documents. Nevertheless, in our experience there is still minor demand of such details. 
 
This may be due to different reasons: 
-Some colaborators do not publish in pure proteomics journals, so with a brieve description of the work done, is enough. 
-Some users are private companies, generaly not interested in publishing and do not demand such information yet. 
 
On top of that, I am afraid that most of users, will not be able to write down the part of proteomics analysis for their papers themselves based on the MIAPE. 
 
If all together manage to get an easy way to send this report, I think it can be useful for general purposes: at home projects, colaborations/services.
Because of I don?t use it frequently, I think that my opinion it isn?t very important, I think it is a good and probably useful application if it?s routinely used in the lab and when you have a complete MIAPE document with all the important data. Now, I don?t dedicate time to implement it because I don?t have enough time between analysis.
No coments
In general the MIAPE compliant reports is a very useful tool both for the customers and for my lab.
In my opinion is a tool very useful both for me and for my users
I think MIAPE compliant reports is a useful tool to arrange the information for a project.
In general, I think is a very usuful tool, but for result report for the customer is very extensive and probably The customers answer us about the means of a lot of the information include in them.