Double MS1 scan before BoxCar scans

[hom...@gmail.com]

Dear all,

we are running BoxCar method with 2 scans and 12 windows using MaxQuant.Live 1.0. We can see that the raw file contains the following order of scans: two regular MS1 scan (i.e. full scan covering all mass range in one go, for example, 350 - 1550), followed by two BoxCar scans (i.e. scans with segmented mass range 375 - 400, 399 - 425, 424 - 450 etc). Previosly, when we did BoxCar aquisition there was only one MS1 scan followed by BoxCar scans (at that time we were using MaxQuant.Live 0.99). In the rawdata from the original BoxCar paper, one can see that there is only one MS1 scan. Thus, it looks like that now we have one "useless" MS1 scan for every cycle.

Is this something one should expect from version 1.0 or it is some kind of bug?

If it is the later case, do anybody else observe additional MS1 scans (so that we can figure out if it is something wrong with our setup)?

Thank you for your help.

Best regards,

Vladimir

[Christoph Wichmann]

Hi Vladimir,

 this can happen if you only have two boxcar scan and no ms2 scans in your cycle. Was this the case in your experiment? The speed API limits the minimal cycle (ms1 scan+boxcar scans + ms2 scans) time. If the cycle is too short, an additional ms1 scan is performed due to technical reasons. Reducing the number of boxcar scans, the number of ms2 scans of the scan resolution can cause these short cycle times. If you would get rid of this behavior you can set the number of boxcar scans to three, for example.

Best,

 Christoph

[hom...@gmail.com]

Hi Christoph,

thank you for clarification. We indeed try to run with short cycle time - the faster the better. Can you share the minimal cycle length that is possible for MaxQuant.Live?

Thank you in advance.

Best regards,

Vladimir