Generally, I obtain something between 700-2800 Da. How can I get smaller fragments? Is it just the type of enzyme we use?
Emilia, part of the answer is in the enzyme, part in your detection system. To get a good idea about different enzymes you can do theoretical digests using the tools present in e.g. uniprot (www.uniprot.org) or Protein Prospector (prospector.ucsf.edu). The resulting peptide set is always a distribution, and a function of enzyme specificity vs. the distribution of cleavage sites in any specific protein sequence. The other part is your detection system - if you are using e.g. LC/MS/MS it will bias against both very short peptides (do not bind to RP, are not identified at high confidence by database search engines as the sequences are not very unique) and very large peptides (pind too well to RP, do not ionize as well, do not fragment specifically/efficiently in MS/MS).
If you definitely want small peptides look toward less specific enzymes, e.g. pepsin or chymotrypsin. It will make identification more challenging though if the termini are variable.
The majority of the double and triple-charged peptides from tryptic digests may be found in the range from 500 to 1500 m/z (but can be higher).. The higher charge peptides like 4+ or 5+ are typically less intensive and can be ommited. The MS/MS data should be aquired in the range from about 50 m/z to as high as mass spectrometer can - when we consider 1500 m/z 3+ peptide it should be at least up to 4500 m/z range.
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