Looking up the Chinese translation of 'What do you mean' in my (pocket) dictionaries and in some translation engines on the internet results in 你是什么意思. In spoken Chinese I hear sounds like 'si mi si' and I'm under the impression that there is some character contraction here. What is the Pinyin pronunciation of 你是什么意思 in spoken Chinese?
Except for established elisions – e.g.
之於 (zhī yú) -> 諸 (zhū),
不用 (bú yòng) -> 甭 (béng),
這一 (zhè yī) -> 這 (zhèi), even if you write out what you hear in pinyin (assuming you followed all the orthographic rules, of course), it is meaningless, because normally you cannot correlate multiple syllables with one character, or multiple characters with one syllable. Pinyin is a system of romanisation, not of phonetic notation.
Using IPA to truthfully record your observation is however acceptable, because it is a rigorous system of phonetic notation. (See how IPA was used in elision studies of Taiwanese Mandarin here) So you may argue a native could understand
[ni˨˩ s/ʂɯ˧˥ mi˥˧ sɯ꜊]or even
[ni˨˩ s/ʂmi˥˧ sɯ꜊]as
你是什麼意思？, but this 1) requires more linguistic proof, 2) is not a 'good' pronunciation (from a prescriptivist point of view), and 3) does not have an equivalent in pinyin.
However, I can support the
什麼 shén me(see here), which may have a role in the elision of your sentence. The dropping of one of the consonants in
是什out of similarity is also likely. Finally,
意begins with a semivowel, which may also facilitate its merging with the previous consonant