Masadaki kalem senin mi?

Masadaki is built from:

• masa = table
• -da = in/on/at
• -ki = a suffix that turns that location phrase into something like the one that is... or the ... on/in/at ...

So:

• masada = on the table
• masadaki = the one on the table / the ... that is on the table

In this sentence, masadaki kalem means the pen on the table.

Because -ki lets the location describe the noun directly.

Compare:

• masada kalem = there is a pen on the table / a pen is on the table
• masadaki kalem = the pen on the table

So -ki works a bit like a relative phrase in English, turning on the table into an adjective-like modifier of kalem.

Sen means you.

Senin is the possessive/genitive form, meaning your or yours, depending on the sentence.

Here, senin mi? means is it yours?

So:

• sen = you
• senin = your / yours

In this sentence, the pen has already been mentioned, so senin is understood as yours.

Mi is the yes/no question particle.

It turns a statement into a question:

• Masadaki kalem senin. = The pen on the table is yours.
• Masadaki kalem senin mi? = Is the pen on the table yours?

A very important point: mi is written separately from the word before it.

It also changes form by vowel harmony:

• mı
• mi
• mu
• mü

Here it is mi because of vowel harmony with senin.

In Turkish, the verb to be is often not expressed in simple present-tense sentences like this, especially in the 3rd person.

So:

• kalem senin literally looks like the pen yours
• but it means the pen is yours

This is completely normal in Turkish.

When you add mi, you get:

• kalem senin mi? = is the pen yours?

Turkish does not have articles like the and a/an in the same way English does.

Whether something is definite or indefinite is usually understood from context or structure.

Here, masadaki kalem naturally means the pen on the table, because the phrase identifies a specific pen.

If you wanted a pen, Turkish often uses bir:

• bir kalem = a pen

But in masadaki kalem, the modifier already makes it specific.

This is a very natural and neutral word order in Turkish.

It is roughly:

• Masadaki kalem = topic / subject
• senin mi = predicate being questioned

Turkish word order is flexible, but changing it can change the emphasis.

For example:

• Masadaki kalem senin mi? = neutral, natural
• Senin mi masadaki kalem? = more emphasis on yours
• Masadaki kalem mi senin? = emphasis on the pen on the table

So the sentence can change, but the version you have is the most straightforward one.

Because kalem is the subject here, not a direct object.

The ending -i in kalemi can mark a definite direct object, but subjects do not take that ending.

So:

• Masadaki kalem senin mi? = The pen on the table, is it yours?
• Kalemi görüyorum. = I see the pen.
  Here kalemi is the direct object, so the accusative ending appears.

This is a very common point of confusion for English speakers.

Yes. Masadaki can sometimes stand on its own when the noun is understood from context.

For example:

• Masadaki benim. = The one on the table is mine.

So -ki can create a form that behaves a bit like:

• the one on the table
• the thing/person in/on/at ...

In your sentence, though, it is used before kalem to specify which pen.