Matthias Cuykx makes a good point.  In addition, though, you will always see peaks!  No solvent is completely pure and no system is completely clean.  We have  occasionally found that batches of vials have organic impurities.  If these compounds are so low in abundance that they don't show up in the total-ion chromatogram, you probably don't have to worry too much when you begin your experiments.  Nonetheless, to minimize this, we distill our water and sometimes our acetonitrile, and sometimes flush the entire system overnight with isopropanol.

Can you show figures of the TIC and BPI? It might be that the scale is different (i.e. the peaks are not visible in the TIC because of the low abundance of each peak in comparison to the entire profile (sum of all peaks).

Matthias Cuykx makes a good point.  In addition, though, you will always see peaks!  No solvent is completely pure and no system is completely clean.  We have  occasionally found that batches of vials have organic impurities.  If these compounds are so low in abundance that they don't show up in the total-ion chromatogram, you probably don't have to worry too much when you begin your experiments.  Nonetheless, to minimize this, we distill our water and sometimes our acetonitrile, and sometimes flush the entire system overnight with isopropanol.

I second John's points, likely nothing to worry about. I've run into similar 'issues' on our LC-MS system. If you want to further minimize these peaks, you could try air injections (empty vial, septum out) to rule out contaminants from your vials, and/or upgrade to LC-MS (not HPLC) quality water and methanol. Are you adding any acid? 

I agree with Teagen . Also it  is worth checking for tune reports for MS to make sure system that  MS is  free from the contaminations

Totally agree John and Teagen. This is contamination. The most comon is PEG contamination and Nylon contamination. Never use Nylon filters and always PTFE filters for your samples. The most common peaks are 325, 311, 274. The contaminations appears with the less of 14 (CH2).

If you use LC-ms degree solvents the problem could be the water. I was discovering that the problem of contamination the water here was the nylon membrane used in Milliq.

Three times for month (in minimal), do this procediments to keep clean the bottles of solvents:

http://www.waters.com/webassets/cms/support/docs/715001307d_cntrl_cntm.pdf

A good article;

Cyclic Polyamide Oligomers Extracted from Nylon 66 Membrane Filter Disks as a Source of Contamination in Liquid Chromatography/Mass Spectrometry

http://www.sciencedirect.com/science/article/pii/S1044030506000742

The BPI do a base line alignment show peaks that before not show too intense. 

Best regards

You will never get a well resolved peaks of methanol:water (1:1).

Dear All

Please take a look at the chromatograms. The bottom one is TIC of methanol water (1:1) where as the top chromatogram is the BPI of TIC. Please give your comments.

Regards

Khalid

I agree with ALL comments. If you check the m/z of all these peaks, I expect to find that all show same ion due to gradient. At low flow rate + gradient elution, you expect this phenomena due to the delivary of high % of organic content of mobile system in showrt time at low flow rate. If you want to make sure that this profile due to elution program, just inject water. I expect you shall get same profile. If not, then for sure you have impurities or the LC system/inline filters, are dirty.

Dear Mohammad,

not too unusual, but probably too high to work with, as other commentes have already discussed.

It is probably a good idea to find out where it is from, I think htere are some really good ideas above:

NOT ionsource

1) column

2) Injector

3) your solvent lines, pumps

4) Your solvents

1) Have a check on the MS what it is, maybe you can trace it back to the column, if so kick it out put a new one in.

2) wash the needle outside and inside and the loop 20-50 times

3) wash with clean solvent over night

4) get solvent of better quality. - Most suppliers now have HPLC-MS grade. - in my experience it is worth it. especially if operating fullscan.

really use the MS to guide you wht it is, and where it is from...

enjoy the next week ;-)

If it is possible run the gradient without preforming an injection, if you still observe the peaks this your LC system is contaminated.  Next run the gradient after an equilibration time that is 3 to 4 times longer than normal, if the intensity of the peaks increase then it is your water that is contaminated. With contaminated water supply also consider the containers that the water has been stored in or been washed with as detergents always cause problems with LCMS.

I do agree with all the suggestions. From the chromatography, it is obvious to say your system was contaminated. Check the nature of the samples that were analyzed prior to you using the QTof. If they were really dirty samples,  then you might need to flush your system overnight. Just a stupid question, are u sure you were injecting from the intended vial ? This might save you a lot of energy and money if it wasn't the case. Do you reuse your vials?  Maybe use a new vial and check. .