Yes I had seen like Irenotican drug. It's absolutely no fragmentation was observed practically.

What instrument are you using for MS/MS experiments? Is it MALDI or ESI based? What is the mass analyzer, wherein Collison Induced Dissociation (CID) is carried out? Is it an ion trap or quadrupole or a hexapole? In other words, are MS/MS data recorded on a Quadrupole/Time-of-Flight (Q/ToF) or an ion trap connected to ESI or ToF/ToF connected to MALDI? What is the collision gas: Helium or Argon or N2 (nitrogen) or air or Xenon? If the precursor ions of your peptides' MS/MS have been attempted in all the conditions mentioned above and still they do not fragment properly, it suggests that their respective chemical property is perhaps responsible in resisting their dissociation. Some chemical derivatizations on those peptides may be done and then fragmentation of the modified peptide precursor ions can be tried. Else, why not try negative ionization and first check, whether these peptides ionize under negative ionization conditions? If so, those anionic peptide precursors can be subjected to CID and then examined, whether the anions are undergoing fragmentation.

I have experienced fragmentation difficulties with some naturally occurring cyclic peptides containing a depsipeptide bond (viscosin, serrawettin W2, surfactin, etc) where no fragmentation occurred at the highest energy for the MS. We use acidified ESI with an LTQ ion-trap MS. Perhaps increasing the % of acid will hydrolyze the depsipeptide bond resulting in a linear peptide that is more susceptible to fragmentation (IF you have a depsipeptide). 

Good luck.

Why do You think it's hard to fragment the mentioned three ions? I suspect the problem is quite different. The sodium adducts easily dissociate during collisions with CID gas with metal cation loss. It leads to occurring of uncharged peptide species and their neutral fragments which You can not detect. In such situation it's not obvious that You should increase the collision energy. Try to decrease it or substitute sodium with other metals which form more stable adducts.  

By the masses you list and doing a quick calculation, I can see you are trying to fragment sodium adducts: 588 would be the Na adduct of 566,  701 would be Na adduct of 679... Sodium adducts "usually" (with some exceptions) do not fragment under MS-MS conditions.  You can try to convert them into ammonium adducts, which will fragment much better.

Sodium ion adducts of peptides do fragment well. There are many studies about this in the literature. As an example, I am herewith attaching one of my publications, where the sodium ion adducts of neutral peptides having modified N- and C- termini underwent CID well. As Carter Mitchell points out, perhaps in your case you might be trying to fragment sodium ion adducts of cyclic peptides, which might be resistant to undergo CID. If these are cyclic depsipeptides, then saponification reaction needs to be done, which will linearize the cyclic depsipeptide at the ester linkage, thereby mass of the peptide will increase by 18 Da. Subsequently, the linearized peptides' proton and sodium ion adducts can be subjected to CID. Saponification can be tried using a base/alkali, say NaOH.

Dear Carter Mitchell: Regarding fragmentation of natural cyclic depsipeptides, kindly try to go through one of my publications, whose .pdf is attached herewith. Also, try to read the following research articles:

1. Thakur et al., J. Am. Soc. Mass Spectrom. 2009, 20: 2221-8.

2. Pathak et al., J. Am. Soc. Mass Spectrom. 2012, 23: 1716-28.

Thank you Doc. Sabareesh. The instrument I am using is Waters UPLC-QTOF MS system. The collision gas is nitrogen. Trying negative ionization is a good suggestion and I’ll try.

Thank you Doc. Kosyakov. I did suppose the mentioned three bigger ions are sodium adducts. What I was curious about is why the sodium adducts seemed to be much harder to be fragmented than the hydrogen adducts. I think you are right. It is possible that the sodium adducts easily dissociate during collisions with CID gas and that might lead to occurring of uncharged peptide species and their neutral fragments which cannot be detected.

Thank you Doc. Ferrer. I am thinking that what I should do next is to make sure that the three bigger ions I mentioned ARE sodium adducts. If they ARE, I won’t bother on fragmenting them since I can just get the sequence information from the proton adducts. I think a MSMS analysis under negative ion mode will help me in figuring this out.

I am sure they are Na adducts, look at your accurate masses.  The accurate mass difference between a protonated molecule and its sodium adduct  is exactly 21.9820, and your numbers are very close.  Negative ionization is a very good idea, try that too.

Dear Jinmei Xia ,

Here you and somebody agreed and talk about sodium adducts but you should think sodium adduct will readily give fragment in MSMS analysis., yah you never get this higher mass peak in MSMS analysis., because MSMS will give peak for fragment which have one more fragment, so that you have this higher mass peak as like base peak it consider for that no fragments of fragment there (will not be there) Now you clear? i have done more analysis with MSMS and ESI-MSMS, MALDI-TOF-MS, So if you need to check just try ESI-MS so that you will get enough expected peak.., MSMS will only for very minute analysis of you 100%Accuracy., Hope you got it

Good Luck&Regards

R.Selva............

Almost all details given by selva, MSMS will never give response when fragments of fragments not possible.,

One way of checking, whether the signals are due to sodium ion adducts is, to add organic acid to the sample, such as formic acid or acetic acid. By doing so, the intensity of sodium ion adduct peaks can decrease and intensity of protonated ion peaks could increase. If this happens, then, the enhanced signals of protonated ions can be selected as precursor for MS/MS (CID) fragmentation.

I think that the charge remains with the sodium upon collision induced dissociation of your intense parent ions, which explains why you are not able to detect any fragments of this species. I would try to add a few millimolar of ammonium formate or acetate - this shifts the species distribution towards ammonium adduct that usually give miuch better fragmentation (at least with the cyclic peptides included in our multi-target method)