It's best if you don't worry about this too much until the end of the game. Getting the Drone Teleport and Red Coat allow you access to the entire map, as well as making some difficult sections far easier to get through.
You will need to collect:
13 Health Nodes
9 Power Nodes
4 Size Nodes
4 Range Nodes
27 Notes
20 Weapons
16 Tools/Upgrades (only 15 appear in your inventory)
For more details, I suggest you read up on each category on their respective trophy pages.

The 100% Items trophy in Axiom Verge worth 230 pointsAcquire 100% of all weapons, tools, upgrades, and notes.There are two things that need to be kept in mind. 1) If you find a secret world, there are power-ups and upgrades that can be collected. These don't count towards collecting everything but they may still appear in your inventory, throwing off your count. 2) There are Small Health and Power Nodes. When you collect enough of them, they turn into large ones in your inventory. Example: You have 9 Large Health Nodes and 4 Small Health Nodes in your inventory. After collecting another Small Health Node, your inventory will reflect that you've collected 10 Large Health Nodes and 0 Small Health Nodes.
If you hit a dead end where there should be more room, try to teleport through what look like solid walls. If that doesn't work, remember that passwords can open up new sections.
Passwords- In Eribu, start in the 2x2 room in the upper left corner, go up through the breakable bricks, into the next room. At the top, enter "IKKIBU-LABIRU" and a door will open up allowing you to go left. This will bring you around and down behind the four energy beams blocking your path in a different room.
- In Eribu, there will be a hallway leading left and through a checkpoint. Go through here to the next hallway and break through the drill wall in the upper left next to the ceiling. Follow the path to the left as far as you can and you'll eventually find a weapon upgrade behind a thick wall. Use "DINGER-GISBAR" to make the wall thinner.
- In Eribu, in the bottom most 2x2 room, go to the upper left corner of the room (you'll see some weird letters written in the rock above you) and enter "DALKHU-SUBTUM" to open a new path.
- In E-Kur-Mah, you'll enter a large 6x3 vertical room. Enter "ISKART-EHANZU" to open a new path to a blocked off section in the middle of the left side of the room. You'll have to enter this section from the bottom.