The most current explanations are:

• Databases, taxons or pI/Mw ranges are too restrictives, try again with broader ranges.
  Note! Default upper Mw is 100000 Da, may be your protein is bigger? Change the value in the sub-form "Protein".
• Thresholds are too restrictives, in particular your calibration error may be higher than default range for slope and shift. Try again with broader ranges. Change the values in the sub-form "Thresholds".
• P-value is too small, try again with pValue = 1. Change the value in the sub-form "Thresholds".
• The minimum hits is too high, try again with a smaller value. Change the value in the sub-form "Thresholds".
• Check peptide modification and modification mode. If your sample has been treated check that the modification mode is "Fixed" and allow a least 1 for tolerance. Change the values in the sub-form "Peptide".
• Check peptide digestion: ion mode, enzyme, etc.
  Note! If you don't know the ion mode, you can select [M] and add H(+) modification in the list, sub-form "Peptide".
• Some peaks in your sample have very very high intensities, probably they are matrix peaks or calibration peaks ? Try again without these peaks, you may comment them in the list with // at the beginning of the line in the sub-form "Sample".

Yes, in the summary of the best matching proteins there is a link "validate" for each ranked protein, at the end of the line. By clicking on this link for one protein, it will resubmit the search with recalibrated masses in the list, and removed matched masses. In addition thresholds will also be refined accordingly.

You may found relevant citations here.

You may found relevant information here.